diff --git a/CHANGELOG.md b/CHANGELOG.md
index 357e75628..7193363b6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,9 @@
 ### Deprecation (API)
 * The `inspect_nwb` method has been removed. Please use `inspect_nwbfile` or `inspect_nwbfile_object` instead. [#505](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/505)
 
+### New Features
+* Added Zarr support. [#513](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/513)
+
 ### Improvements
 * Removed the `robust_ros3_read` utility helper. [#506](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/506)
 * Simplified the `nwbinspector.testing` configuration framework. [#509](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/509)
diff --git a/MANIFEST.in b/MANIFEST.in
index f8ca9e67f..6f5bd76e7 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,5 +1,4 @@
 graft tests
 global-exclude *.py[cod]
-include src/nwbinspector/internal_configs/dandi.inspector_config.yaml
-include src/nwbinspector/config.schema.json
-include requirements.txt
+include src/nwbinspector/_internal_configs/dandi.inspector_config.yaml
+include src/nwbinspector/_internal_configs/config.schema.json
diff --git a/src/nwbinspector/__init__.py b/src/nwbinspector/__init__.py
index 4c5f6a3d6..0f21d7c29 100644
--- a/src/nwbinspector/__init__.py
+++ b/src/nwbinspector/__init__.py
@@ -26,6 +26,10 @@
 # Still keeping the legacy magic version attribute requested by some users
 __version__ = importlib.metadata.version(distribution_name="nwbinspector")
 
+# Note: this is not exposed at this outer level, but is used here to trigger the automatic submodule import
+# (otherwise someone would have to import nwbinspector.testing explicitly)
+from .testing import check_streaming_tests_enabled  # noqa: F401
+
 __all__ = [
     "available_checks",
     "default_check_registry",
@@ -51,4 +55,8 @@
     "FormatterOptions",
     "organize_messages",
     "__version__",
+    # Public submodules
+    "checks",
+    "testing",
+    "utils",
 ]
diff --git a/src/nwbinspector/_configuration.py b/src/nwbinspector/_configuration.py
index b8692fe64..c5d3995e6 100644
--- a/src/nwbinspector/_configuration.py
+++ b/src/nwbinspector/_configuration.py
@@ -13,12 +13,15 @@
 from . import available_checks
 from ._registration import Importance
 
-INTERNAL_CONFIGS = dict(dandi=Path(__file__).parent / "internal_configs" / "dandi.inspector_config.yaml")
+INTERNAL_CONFIGS = dict(
+    dandi=Path(__file__).parent / "_internal_configs" / "dandi.inspector_config.yaml",
+)
 
 
 def validate_config(config: dict):
     """Validate an instance of configuration against the official schema."""
-    with open(file=Path(__file__).parent / "config.schema.json", mode="r") as fp:
+    config_schema_file_path = Path(__file__).parent / "_internal_configs" / "config.schema.json"
+    with open(file=config_schema_file_path, mode="r") as fp:
         schema = json.load(fp=fp)
     jsonschema.validate(instance=config, schema=schema)
 
diff --git a/src/nwbinspector/config.schema.json b/src/nwbinspector/_internal_configs/config.schema.json
similarity index 100%
rename from src/nwbinspector/config.schema.json
rename to src/nwbinspector/_internal_configs/config.schema.json
diff --git a/src/nwbinspector/internal_configs/dandi.inspector_config.yaml b/src/nwbinspector/_internal_configs/dandi.inspector_config.yaml
similarity index 100%
rename from src/nwbinspector/internal_configs/dandi.inspector_config.yaml
rename to src/nwbinspector/_internal_configs/dandi.inspector_config.yaml
diff --git a/src/nwbinspector/_nwb_inspection.py b/src/nwbinspector/_nwb_inspection.py
index 400f26b36..55406998e 100644
--- a/src/nwbinspector/_nwb_inspection.py
+++ b/src/nwbinspector/_nwb_inspection.py
@@ -12,8 +12,10 @@
 from natsort import natsorted
 from tqdm import tqdm
 
-from . import available_checks, configure_checks
+from . import available_checks
+from ._configuration import configure_checks
 from ._registration import Importance, InspectorMessage
+from .tools._read_nwbfile import read_nwbfile
 from .utils import (
     FilePathType,
     OptionalListOfStrings,
@@ -127,7 +129,7 @@ def inspect_all(
         progress_bar_options = dict(position=0, leave=False)
 
     if in_path.is_dir():
-        nwbfiles = list(in_path.rglob("*.nwb"))
+        nwbfiles = list(in_path.rglob("*.nwb*"))
 
         # Remove any macOS sidecar files
         nwbfiles = [nwbfile for nwbfile in nwbfiles if not nwbfile.name.startswith("._")]
@@ -141,17 +143,16 @@ def inspect_all(
     # Manual identifier check over all files in the folder path
     identifiers = defaultdict(list)
     for nwbfile_path in nwbfiles:
-        with pynwb.NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
-            try:
-                nwbfile = io.read()
-                identifiers[nwbfile.identifier].append(nwbfile_path)
-            except Exception as exception:
-                yield InspectorMessage(
-                    message=traceback.format_exc(),
-                    importance=Importance.ERROR,
-                    check_function_name=f"During io.read() - {type(exception)}: {str(exception)}",
-                    file_path=nwbfile_path,
-                )
+        try:
+            nwbfile = read_nwbfile(nwbfile_path=nwbfile_path)
+            identifiers[nwbfile.identifier].append(nwbfile_path)
+        except Exception as exception:
+            yield InspectorMessage(
+                message=traceback.format_exc(),
+                importance=Importance.ERROR,
+                check_function_name=f"During io.read() - {type(exception)}: {str(exception)}",
+                file_path=nwbfile_path,
+            )
 
     if len(identifiers) != len(nwbfiles):
         for identifier, nwbfiles_with_identifier in identifiers.items():
@@ -198,7 +199,7 @@ def inspect_all(
                     yield message
     else:
         for nwbfile_path in nwbfiles_iterable:
-            for message in inspect_nwbfile(nwbfile_path=nwbfile_path, checks=checks):
+            for message in inspect_nwbfile(nwbfile_path=nwbfile_path, checks=checks, skip_validate=skip_validate):
                 yield message
 
 
@@ -237,7 +238,7 @@ def inspect_nwbfile(
     config : dict
         Dictionary valid against our JSON configuration schema.
         Can specify a mapping of importance levels and list of check functions whose importance you wish to change.
-        Typically loaded via json.load from a valid .json file
+        Typically loaded via `json.load` from a valid .json file.
     ignore: list, optional
         Names of functions to skip.
     select: list, optional
@@ -267,10 +268,12 @@ def inspect_nwbfile(
     filterwarnings(action="ignore", message="No cached namespaces found in .*")
     filterwarnings(action="ignore", message="Ignoring cached namespace .*")
 
-    if not skip_validate:
-        validation_error_list, _ = pynwb.validate(paths=[nwbfile_path])
-        for validation_namespace_errors in validation_error_list:
-            for validation_error in validation_namespace_errors:
+    try:
+        in_memory_nwbfile, io = read_nwbfile(nwbfile_path=nwbfile_path, return_io=True)
+
+        if not skip_validate:
+            validation_errors = pynwb.validate(io=io)
+            for validation_error in validation_errors:
                 yield InspectorMessage(
                     message=validation_error.reason,
                     importance=Importance.PYNWB_VALIDATION,
@@ -279,27 +282,23 @@ def inspect_nwbfile(
                     file_path=nwbfile_path,
                 )
 
-    with pynwb.NWBHDF5IO(path=nwbfile_path, mode="r", load_namespaces=True) as io:
-        try:
-            in_memory_nwbfile = io.read()
-
-            for inspector_message in inspect_nwbfile_object(
-                nwbfile_object=in_memory_nwbfile,
-                checks=checks,
-                config=config,
-                ignore=ignore,
-                select=select,
-                importance_threshold=importance_threshold,
-            ):
-                inspector_message.file_path = nwbfile_path
-                yield inspector_message
-        except Exception as exception:
-            yield InspectorMessage(
-                message=traceback.format_exc(),
-                importance=Importance.ERROR,
-                check_function_name=f"During io.read() - {type(exception)}: {str(exception)}",
-                file_path=nwbfile_path,
-            )
+        for inspector_message in inspect_nwbfile_object(
+            nwbfile_object=in_memory_nwbfile,
+            checks=checks,
+            config=config,
+            ignore=ignore,
+            select=select,
+            importance_threshold=importance_threshold,
+        ):
+            inspector_message.file_path = nwbfile_path
+            yield inspector_message
+    except Exception as exception:
+        yield InspectorMessage(
+            message=traceback.format_exc(),
+            importance=Importance.ERROR,
+            check_function_name=f"During io.read() - {type(exception)}: {str(exception)}",
+            file_path=nwbfile_path,
+        )
 
 
 # TODO: deprecate once subject types and dandi schemas have been extended
diff --git a/src/nwbinspector/_registration.py b/src/nwbinspector/_registration.py
index e772a413f..5ce7fa515 100644
--- a/src/nwbinspector/_registration.py
+++ b/src/nwbinspector/_registration.py
@@ -4,6 +4,7 @@
 from typing import Optional
 
 import h5py
+import zarr
 from pynwb import NWBFile
 from pynwb.ecephys import Device, ElectrodeGroup
 from pynwb.file import Subject
@@ -93,7 +94,7 @@ def _auto_parse(check_function, obj, result: Optional[InspectorMessage] = None):
 
 
 def _parse_location(neurodata_object) -> Optional[str]:
-    """Grab the object location from a h5py.Dataset or a container content that is an h5py.Dataset object."""
+    """Grab the object location from a dataset or a container content that is an dataset object."""
     known_locations = {
         NWBFile: "/",
         Subject: "/general/subject",
@@ -105,13 +106,16 @@ def _parse_location(neurodata_object) -> Optional[str]:
     for key, val in known_locations.items():
         if isinstance(neurodata_object, key):
             return val
-    """Infer the human-readable path of the object within an NWBFile by tracing its parents."""
+
+    # Infer the human-readable path of the object within an NWBFile by tracing its parents
     if neurodata_object.parent is None:
         return "/"
     # Best solution: object is or has a HDF5 Dataset
-    if isinstance(neurodata_object, h5py.Dataset):
+    if isinstance(neurodata_object, (h5py.Dataset, zarr.Array)):
         return neurodata_object.name
     else:
-        for field in neurodata_object.fields.values():
+        for field_name, field in neurodata_object.fields.items():
             if isinstance(field, h5py.Dataset):
                 return field.parent.name
+            elif isinstance(field, zarr.Array):
+                return field.name.removesuffix(f"/{field_name}")
diff --git a/src/nwbinspector/checks/_nwb_containers.py b/src/nwbinspector/checks/_nwb_containers.py
index 8f8861d6e..2d45c39fa 100644
--- a/src/nwbinspector/checks/_nwb_containers.py
+++ b/src/nwbinspector/checks/_nwb_containers.py
@@ -3,6 +3,7 @@
 import os
 
 import h5py
+import zarr
 from pynwb import NWBContainer
 
 from .._registration import Importance, InspectorMessage, Severity, register_check
@@ -19,9 +20,16 @@ def check_large_dataset_compression(nwb_container: NWBContainer, gb_lower_bound:
     Best Practice: :ref:`best_practice_compression`
     """
     for field in getattr(nwb_container, "fields", dict()).values():
-        if not isinstance(field, h5py.Dataset):
+        if not isinstance(field, (h5py.Dataset, zarr.Array)):
             continue
-        if field.compression is None and field.size * field.dtype.itemsize > gb_lower_bound * 1e9:
+
+        compression_indicator = None
+        if isinstance(field, h5py.Dataset):
+            compression_indicator = field.compression
+        elif isinstance(field, zarr.Array):
+            compression_indicator = field.compressor
+
+        if compression_indicator is not None and field.size * field.dtype.itemsize > gb_lower_bound * 1e9:
             return InspectorMessage(
                 severity=Severity.HIGH,
                 message=f"{os.path.split(field.name)[1]} is a large uncompressed dataset! Please enable compression.",
@@ -44,10 +52,17 @@ def check_small_dataset_compression(
     Best Practice: :ref:`best_practice_compression`
     """
     for field in getattr(nwb_container, "fields", dict()).values():
-        if not isinstance(field, h5py.Dataset):
+        if not isinstance(field, (h5py.Dataset, zarr.Array)):
             continue
+
+        compression_indicator = None
+        if isinstance(field, h5py.Dataset):
+            compression_indicator = field.compression
+        elif isinstance(field, zarr.Array):
+            compression_indicator = field.compressor
+
         if (
-            field.compression is None
+            compression_indicator is None
             and mb_lower_bound * 1e6 < field.size * field.dtype.itemsize < gb_upper_bound * 1e9
         ):
             if field.size * field.dtype.itemsize > gb_severity_threshold * 1e9:
diff --git a/src/nwbinspector/tools/__init__.py b/src/nwbinspector/tools/__init__.py
index cac8b0683..674f827a2 100644
--- a/src/nwbinspector/tools/__init__.py
+++ b/src/nwbinspector/tools/__init__.py
@@ -1,8 +1,9 @@
 from ._dandi import get_s3_urls_and_dandi_paths
 from ._nwb import all_of_type, get_nwbfile_path_from_internal_object
-from ._read_nwbfile import read_nwbfile
+from ._read_nwbfile import BACKEND_IO_CLASSES, read_nwbfile
 
 __all__ = [
+    "BACKEND_IO_CLASSES",
     "get_s3_urls_and_dandi_paths",
     "all_of_type",
     "get_nwbfile_path_from_internal_object",
diff --git a/src/nwbinspector/tools/_read_nwbfile.py b/src/nwbinspector/tools/_read_nwbfile.py
index 07d61d802..20fe30b08 100644
--- a/src/nwbinspector/tools/_read_nwbfile.py
+++ b/src/nwbinspector/tools/_read_nwbfile.py
@@ -5,17 +5,14 @@
 from warnings import filterwarnings
 
 import h5py
+from hdmf.backends.io import HDMFIO
+from hdmf_zarr import NWBZarrIO
 from pynwb import NWBHDF5IO, NWBFile
 
-_BACKEND_IO_CLASSES = dict(hdf5=NWBHDF5IO)
-
-try:
-    from hdmf_zarr import NWBZarrIO
-
-    _BACKEND_IO_CLASSES.update(zarr=NWBZarrIO)
-except ModuleNotFoundError as exception:
-    if str(exception) != "No module named 'hdmf_zarr'":  # not the exception we're looking for, so re-raise
-        raise exception
+BACKEND_IO_CLASSES = dict(
+    hdf5=NWBHDF5IO,
+    zarr=NWBZarrIO,
+)
 
 
 def _get_method(path: str):
@@ -47,11 +44,11 @@ def _get_backend(path: str, method: Literal["local", "fsspec", "ros3"]):
     if method == "fsspec":
         fs = _init_fsspec(path=path)
         with fs.open(path=path, mode="rb") as file:
-            for backend_name, backend_class in _BACKEND_IO_CLASSES.items():
+            for backend_name, backend_class in BACKEND_IO_CLASSES.items():
                 if backend_class.can_read(path=file):
                     possible_backends.append(backend_name)
     else:
-        for backend_name, backend_class in _BACKEND_IO_CLASSES.items():
+        for backend_name, backend_class in BACKEND_IO_CLASSES.items():
             if backend_class.can_read(path):
                 possible_backends.append(backend_name)
 
@@ -69,7 +66,8 @@ def read_nwbfile(
     nwbfile_path: Union[str, Path],
     method: Optional[Literal["local", "fsspec", "ros3"]] = None,
     backend: Optional[Literal["hdf5", "zarr"]] = None,
-) -> NWBFile:
+    return_io: bool = False,
+) -> Union[NWBFile, tuple[NWBFile, HDMFIO]]:
     """
     Read an NWB file using the specified (or auto-detected) method and specified (or auto-detected) backend.
 
@@ -85,10 +83,16 @@ def read_nwbfile(
     backend : "hdf5", "zarr", or None (default)
         Type of backend used to write the file.
         The default auto-detects the type of the file.
+    return_io : bool, default: False
+        Whether to return the HDMFIO object used to open the file.
 
     Returns
     -------
-    pynwb.NWBFile
+    nwbfile : pynwb.NWBFile
+        The in-memory NWBFile object.
+    io : hdmf.backends.io.HDMFIO, optional
+        Only passed if `return_io` is True.
+        The initialized HDMFIO object used to read the file.
     """
     nwbfile_path = str(nwbfile_path)  # If pathlib.Path, cast to str; if already str, no harm done
 
@@ -109,7 +113,7 @@ def read_nwbfile(
         )
 
     backend = backend or _get_backend(nwbfile_path, method)
-    if method == "local" and not _BACKEND_IO_CLASSES[  # Temporary until .can_read() is able to work on streamed bytes
+    if method == "local" and not BACKEND_IO_CLASSES[  # Temporary until .can_read() is able to work on streamed bytes
         backend
     ].can_read(path=nwbfile_path):
         raise IOError(f"The chosen backend ({backend}) is unable to read the file! Please select a different backend.")
@@ -127,7 +131,10 @@ def read_nwbfile(
         io_kwargs.update(path=nwbfile_path)
     if method == "ros3":
         io_kwargs.update(driver="ros3")
-    io = _BACKEND_IO_CLASSES[backend](**io_kwargs)
+    io = BACKEND_IO_CLASSES[backend](**io_kwargs)
     nwbfile = io.read()
 
-    return nwbfile
+    if return_io:
+        return (nwbfile, io)
+    else:  # Note: do not be concerned about io object closing due to garbage collection here
+        return nwbfile  # (it is attached as an attribute to the NWBFile object)
diff --git a/src/nwbinspector/utils/_utils.py b/src/nwbinspector/utils/_utils.py
index a0f06661f..a1fddd411 100644
--- a/src/nwbinspector/utils/_utils.py
+++ b/src/nwbinspector/utils/_utils.py
@@ -10,6 +10,7 @@
 
 import h5py
 import numpy as np
+import zarr
 from hdmf.backends.hdf5.h5_utils import H5Dataset
 from numpy.typing import ArrayLike
 from packaging import version
@@ -25,7 +26,7 @@
 
 @lru_cache(maxsize=MAX_CACHE_ITEMS)
 def _cache_data_retrieval_command(
-    data: h5py.Dataset, reduced_selection: tuple[tuple[Optional[int], Optional[int], Optional[int]]]
+    data: Union[h5py.Dataset, zarr.Array], reduced_selection: tuple[tuple[Optional[int], Optional[int], Optional[int]]]
 ) -> np.ndarray:
     """LRU caching for _cache_data_selection cannot be applied to list inputs; this expects the tuple or Dataset."""
     selection = tuple([slice(*reduced_slice) for reduced_slice in reduced_selection])  # reconstitute the slices
diff --git a/tests/000126_report.txt b/tests/expected_reports/000126_report.txt
similarity index 100%
rename from tests/000126_report.txt
rename to tests/expected_reports/000126_report.txt
diff --git a/tests/true_nwbinspector_default_report.txt b/tests/expected_reports/true_nwbinspector_default_report_hdf5.txt
similarity index 65%
rename from tests/true_nwbinspector_default_report.txt
rename to tests/expected_reports/true_nwbinspector_default_report_hdf5.txt
index aa0447eba..8fd1cefe5 100644
--- a/tests/true_nwbinspector_default_report.txt
+++ b/tests/expected_reports/true_nwbinspector_default_report_hdf5.txt
@@ -15,20 +15,20 @@ Found 5 issues over 2 files:
 0  CRITICAL
 ===========
 
-0.0  ./testing0.nwb: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
+0.0  ./testing0.nwb.hdf5: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
        Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
 
-0.1  ./testing0.nwb: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+0.1  ./testing0.nwb.hdf5: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
        Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
 
 1  BEST_PRACTICE_VIOLATION
 ==========================
 
-1.2  ./testing0.nwb and 1 other file: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+1.2  ./testing0.nwb.hdf5 and 1 other file: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
        Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.
 
 2  BEST_PRACTICE_SUGGESTION
 ===========================
 
-2.3  ./testing0.nwb: check_small_dataset_compression - 'TimeSeries' object at location '/acquisition/test_time_series_1'
+2.3  ./testing0.nwb.hdf5: check_small_dataset_compression - 'TimeSeries' object at location '/acquisition/test_time_series_1'
        Message: data is not compressed. Consider enabling compression when writing a dataset.
diff --git a/tests/expected_reports/true_nwbinspector_default_report_zarr.txt b/tests/expected_reports/true_nwbinspector_default_report_zarr.txt
new file mode 100644
index 000000000..957e68adc
--- /dev/null
+++ b/tests/expected_reports/true_nwbinspector_default_report_zarr.txt
@@ -0,0 +1,34 @@
+**************************************************
+NWBInspector Report Summary
+
+Timestamp: 2022-04-01 13:32:13.756390-04:00
+Platform: Windows-10-10.0.19043-SP0
+NWBInspector version: 0.3.6
+
+Found 5 issues over 2 files:
+       2 - CRITICAL
+       2 - BEST_PRACTICE_VIOLATION
+       1 - BEST_PRACTICE_SUGGESTION
+**************************************************
+
+
+0  CRITICAL
+===========
+
+0.0  ./testing0.nwb.zarr: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
+       Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
+
+0.1  ./testing0.nwb.zarr: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+       Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
+
+1  BEST_PRACTICE_VIOLATION
+==========================
+
+1.2  ./testing0.nwb.zarr and 1 other file: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+       Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.
+
+2  BEST_PRACTICE_SUGGESTION
+===========================
+
+2.3  ./testing0.nwb.zarr: check_small_dataset_compression - 'TimeSeries' object at location '/acquisition/test_time_series_1'
+       Message: data is not compressed. Consider enabling compression when writing a dataset.
diff --git a/tests/true_nwbinspector_report_with_dandi_config.txt b/tests/expected_reports/true_nwbinspector_report_with_dandi_config_hdf5.txt
similarity index 58%
rename from tests/true_nwbinspector_report_with_dandi_config.txt
rename to tests/expected_reports/true_nwbinspector_report_with_dandi_config_hdf5.txt
index e6f80f0f1..4b282018b 100644
--- a/tests/true_nwbinspector_report_with_dandi_config.txt
+++ b/tests/expected_reports/true_nwbinspector_report_with_dandi_config_hdf5.txt
@@ -14,32 +14,32 @@ Found 10 issues over 2 files:
 0  CRITICAL
 ===========
 
-0.0  ./testing0.nwb and 1 other file: check_subject_exists - 'NWBFile' object at location '/'
+0.0  ./testing0.nwb.hdf5 and 1 other file: check_subject_exists - 'NWBFile' object at location '/'
        Message: Subject is missing.
 
-0.1  ./testing0.nwb: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+0.1  ./testing0.nwb.hdf5: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
        Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
 
 1  BEST_PRACTICE_VIOLATION
 ==========================
 
-1.2  ./testing0.nwb: check_time_interval_time_columns - 'TimeIntervals' object with name 'test_table'
+1.2  ./testing0.nwb.hdf5: check_time_interval_time_columns - 'TimeIntervals' object with name 'test_table'
        Message: ['start_time'] are time columns but the values are not in ascending order. All times should be in seconds with respect to the session start time.
 
-1.3  ./testing0.nwb: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+1.3  ./testing0.nwb.hdf5: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
        Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.
 
-1.4  ./testing0.nwb: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
+1.4  ./testing0.nwb.hdf5: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
        Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
 
-1.5  ./testing0.nwb: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+1.5  ./testing0.nwb.hdf5: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_3'
        Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
 
-1.6  ./testing0.nwb: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+1.6  ./testing0.nwb.hdf5: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_2'
        Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
 
-1.7  ./testing0.nwb: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_1'
+1.7  ./testing0.nwb.hdf5: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_1'
        Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
 
-1.8  ./testing1.nwb: check_data_orientation - 'TimeSeries' object at location '/acquisition/my_spatial_series'
+1.8  ./testing1.nwb.hdf5: check_data_orientation - 'TimeSeries' object at location '/acquisition/my_spatial_series'
        Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
diff --git a/tests/expected_reports/true_nwbinspector_report_with_dandi_config_zarr.txt b/tests/expected_reports/true_nwbinspector_report_with_dandi_config_zarr.txt
new file mode 100644
index 000000000..934b7e5fb
--- /dev/null
+++ b/tests/expected_reports/true_nwbinspector_report_with_dandi_config_zarr.txt
@@ -0,0 +1,45 @@
+**************************************************
+NWBInspector Report Summary
+
+Timestamp: 2022-04-01 13:32:13.756390-04:00
+Platform: Windows-10-10.0.19043-SP0
+NWBInspector version: 0.3.6
+
+Found 10 issues over 2 files:
+       3 - CRITICAL
+       7 - BEST_PRACTICE_VIOLATION
+**************************************************
+
+
+0  CRITICAL
+===========
+
+0.0  ./testing0.nwb.zarr and 1 other file: check_subject_exists - 'NWBFile' object at location '/'
+       Message: Subject is missing.
+
+0.1  ./testing0.nwb.zarr: check_timestamps_match_first_dimension - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+       Message: The length of the first dimension of data (4) does not match the length of timestamps (3).
+
+1  BEST_PRACTICE_VIOLATION
+==========================
+
+1.2  ./testing0.nwb.zarr: check_time_interval_time_columns - 'TimeIntervals' object with name 'test_table'
+       Message: ['start_time'] are time columns but the values are not in ascending order. All times should be in seconds with respect to the session start time.
+
+1.3  ./testing0.nwb.zarr: check_regular_timestamps - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+       Message: TimeSeries appears to have a constant sampling rate. Consider specifying starting_time=1.2 and rate=0.5 instead of timestamps.
+
+1.4  ./testing0.nwb.zarr: check_data_orientation - 'SpatialSeries' object at location '/processing/behavior/Position/my_spatial_series'
+       Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
+
+1.5  ./testing0.nwb.zarr: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_3'
+       Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
+
+1.6  ./testing0.nwb.zarr: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_2'
+       Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
+
+1.7  ./testing0.nwb.zarr: check_missing_unit - 'TimeSeries' object at location '/acquisition/test_time_series_1'
+       Message: Missing text for attribute 'unit'. Please specify the scientific unit of the 'data'.
+
+1.8  ./testing1.nwb.zarr: check_data_orientation - 'TimeSeries' object at location '/acquisition/my_spatial_series'
+       Message: Data may be in the wrong orientation. Time should be in the first dimension, and is usually the longest dimension. Here, another dimension is longer.
diff --git a/tests/streaming_cli_tests.py b/tests/streaming_cli_tests.py
index e8e91d38d..7f116d0c8 100644
--- a/tests/streaming_cli_tests.py
+++ b/tests/streaming_cli_tests.py
@@ -10,6 +10,7 @@
 from nwbinspector.testing import check_streaming_tests_enabled
 
 STREAMING_TESTS_ENABLED, DISABLED_STREAMING_TESTS_REASON = check_streaming_tests_enabled()
+EXPECTED_REPORTS_FOLDER_PATH = Path(__file__).parent / "expected_reports"
 
 
 @pytest.mark.skipif(not STREAMING_TESTS_ENABLED, reason=DISABLED_STREAMING_TESTS_REASON or "")
@@ -24,7 +25,7 @@ def test_dandiset_streaming_cli(tmpdir: py.path.local):
     with open(file=console_output_file_path, mode="r") as io:
         test_console_output = io.readlines()
 
-    expected_output_file_path = Path(__file__).parent / "000126_report.txt"
+    expected_output_file_path = EXPECTED_REPORTS_FOLDER_PATH / "000126_report.txt"
     with open(file=expected_output_file_path, mode="r") as io:
         expected_console_output = io.readlines()
 
@@ -47,7 +48,7 @@ def test_dandiset_streaming_cli_with_version(tmpdir: py.path.local):
     with open(file=console_output_file_path, mode="r") as io:
         test_console_output = io.readlines()
 
-    expected_output_file_path = Path(__file__).parent / "000126_report.txt"
+    expected_output_file_path = EXPECTED_REPORTS_FOLDER_PATH / "000126_report.txt"
     with open(file=expected_output_file_path, mode="r") as io:
         expected_console_output = io.readlines()
 
@@ -77,7 +78,7 @@ def test_dandiset_streaming_cli_saved_report(tmpdir: py.path.local):
     with open(file=report_file_path, mode="r") as io:
         test_report = io.readlines()
 
-    expected_report_file_path = Path(__file__).parent / "000126_report.txt"
+    expected_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "000126_report.txt"
     with open(file=expected_report_file_path, mode="r") as io:
         expected_report = io.readlines()
 
@@ -110,7 +111,7 @@ def test_dandiset_streaming_cli_with_version_saved_report(tmpdir: py.path.local)
     with open(file=report_file_path, mode="r") as io:
         test_report = io.readlines()
 
-    expected_report_file_path = Path(__file__).parent / "000126_report.txt"
+    expected_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "000126_report.txt"
     with open(file=expected_report_file_path, mode="r") as io:
         expected_report = io.readlines()
 
diff --git a/tests/test_inspector.py b/tests/test_inspector.py
index aa0896258..b3d86c916 100644
--- a/tests/test_inspector.py
+++ b/tests/test_inspector.py
@@ -3,12 +3,15 @@
 from pathlib import Path
 from shutil import rmtree
 from tempfile import mkdtemp
+from typing import Type
 from unittest import TestCase
 
+import hdmf_zarr
 import numpy as np
+from hdmf.backends.io import HDMFIO
 from hdmf.common import DynamicTable
 from natsort import natsorted
-from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+from pynwb import NWBFile, TimeSeries
 from pynwb.behavior import Position, SpatialSeries
 from pynwb.file import Subject, TimeIntervals
 
@@ -31,10 +34,33 @@
     check_timestamps_match_first_dimension,
 )
 from nwbinspector.testing import make_minimal_nwbfile
+from nwbinspector.tools import BACKEND_IO_CLASSES
 from nwbinspector.utils import FilePathType
 
+IO_CLASSES_TO_BACKEND = {v: k for k, v in BACKEND_IO_CLASSES.items()}
+EXPECTED_REPORTS_FOLDER_PATH = Path(__file__).parent / "expected_reports"
+
+
+@register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=DynamicTable)
+def iterable_check_function(table: DynamicTable):
+    for col in table.columns:
+        yield InspectorMessage(message=f"Column: {col.name}")
+
+
+def add_big_dataset_no_compression(nwbfile: NWBFile, zarr: bool = False) -> None:
+    # Zarr automatically compresses by default
+    # So to get a test case that is not compressed, forcibly disable the compressor
+    if zarr:
+        time_series = TimeSeries(
+            name="test_time_series_1",
+            data=hdmf_zarr.ZarrDataIO(np.zeros(shape=int(1.1e9 / np.dtype("float").itemsize)), compressor=False),
+            rate=1.0,
+            unit="",
+        )
+        nwbfile.add_acquisition(time_series)
+
+        return
 
-def add_big_dataset_no_compression(nwbfile: NWBFile):
     time_series = TimeSeries(
         name="test_time_series_1", data=np.zeros(shape=int(1.1e9 / np.dtype("float").itemsize)), rate=1.0, unit=""
     )
@@ -85,8 +111,11 @@ def add_simple_table(nwbfile: NWBFile):
     nwbfile.add_acquisition(time_intervals)
 
 
-class TestInspector(TestCase):
-    """A common helper class for testing the NWBInspector."""
+class TestInspectorOnBackend(TestCase):
+    """A common helper class for testing the NWBInspector on files of a specific backend (HDF5 or Zarr)."""
+
+    BackendIOClass: Type[HDMFIO]
+    skip_validate = False  # TODO: can be removed once NWBZarrIO validation issues are resolved
 
     @staticmethod
     def assertFileExists(path: FilePathType):
@@ -94,37 +123,49 @@ def assertFileExists(path: FilePathType):
         assert path.exists()
 
     def assertLogFileContentsEqual(
-        self, test_file_path: FilePathType, true_file_path: FilePathType, skip_first_newlines: bool = False
+        self,
+        test_file_path: FilePathType,
+        true_file_path: FilePathType,
+        skip_first_newlines: bool = True,
+        skip_last_newlines: bool = True,
     ):
-        skip_first_n_lines = 0
         with open(file=test_file_path, mode="r") as test_file:
-            test_file_lines = test_file.readlines()
+            test_file_lines = [x.rstrip("\n") for x in test_file.readlines()]
         with open(file=true_file_path, mode="r") as true_file:
-            true_file_lines = true_file.readlines()
+            true_file_lines = [x.rstrip("\n") for x in true_file.readlines()]
 
+        skip_first_n_lines = 0
         if skip_first_newlines:
             for line_number, test_line in enumerate(test_file_lines):
-                if test_line != "\n":
+                if len(test_line) > 8:  # Can sometimes be a CLI specific byte such as '\x1b[0m\x1b[0m'
                     skip_first_n_lines = line_number
                     break
-        else:
-            skip_first_n_lines = 0
+
+        skip_last_n_lines = 0
+        if skip_last_newlines:
+            for line_number, test_line in enumerate(test_file_lines[::-1]):
+                if len(test_line) > 4:  # Can sometimes be a CLI specific byte such as '\x1b[0m'
+                    skip_last_n_lines = line_number - 1  # Adjust for negative slicing
+                    break
 
         for line_number, test_line in enumerate(test_file_lines):
             if "Timestamp: " in test_line:
                 # Transform the test file header to match ground true example
-                test_file_lines[line_number] = "Timestamp: 2022-04-01 13:32:13.756390-04:00\n"
-                test_file_lines[line_number + 1] = "Platform: Windows-10-10.0.19043-SP0\n"
-                test_file_lines[line_number + 2] = "NWBInspector version: 0.3.6\n"
+                test_file_lines[line_number] = "Timestamp: 2022-04-01 13:32:13.756390-04:00"
+                test_file_lines[line_number + 1] = "Platform: Windows-10-10.0.19043-SP0"
+                test_file_lines[line_number + 2] = "NWBInspector version: 0.3.6"
             if ".nwb" in test_line:
                 # Transform temporary testing path and formatted to hardcoded fake path
                 str_loc = test_line.find(".nwb")
                 correction_str = test_line.replace(test_line[5 : str_loc - 8], "./")  # noqa: E203 (black)
                 test_file_lines[line_number] = correction_str
-        self.assertEqual(first=test_file_lines[skip_first_n_lines:-1], second=true_file_lines)
+        self.assertEqual(first=test_file_lines[skip_first_n_lines : -(1 + skip_last_n_lines)], second=true_file_lines)
 
 
-class TestInspectorAPI(TestInspector):
+class TestInspectorAPIAndCLIHDF5(TestInspectorOnBackend):
+    BackendIOClass = BACKEND_IO_CLASSES["hdf5"]
+    skip_validate = False
+    true_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "true_nwbinspector_default_report_hdf5.txt"
     maxDiff = None
 
     @classmethod
@@ -140,7 +181,7 @@ def setUpClass(cls):
         nwbfiles = list()
         for j in range(num_nwbfiles):
             nwbfiles.append(make_minimal_nwbfile())
-        add_big_dataset_no_compression(nwbfiles[0])
+        add_big_dataset_no_compression(nwbfiles[0], zarr=cls.BackendIOClass is BACKEND_IO_CLASSES["zarr"])
         add_regular_timestamps(nwbfiles[0])
         add_flipped_data_orientation_to_processing(nwbfiles[0])
         add_non_matching_timestamps_dimension(nwbfiles[0])
@@ -149,18 +190,21 @@ def setUpClass(cls):
         # Third file to be left without violations
         add_non_matching_timestamps_dimension(nwbfiles[3])
 
-        cls.nwbfile_paths = [str(cls.tempdir / f"testing{j}.nwb") for j in range(num_nwbfiles)]
+        suffix = IO_CLASSES_TO_BACKEND[cls.BackendIOClass]
+        cls.nwbfile_paths = [str(cls.tempdir / f"testing{j}.nwb.{suffix}") for j in range(num_nwbfiles)]
         cls.nwbfile_paths[3] = str(cls.tempdir / "._testing3.nwb")
         for nwbfile_path, nwbfile in zip(cls.nwbfile_paths, nwbfiles):
-            with NWBHDF5IO(path=nwbfile_path, mode="w") as io:
+            with cls.BackendIOClass(path=nwbfile_path, mode="w") as io:
                 io.write(nwbfile)
 
     @classmethod
     def tearDownClass(cls):
-        rmtree(cls.tempdir)
+        rmtree(cls.tempdir, ignore_errors=True)
 
     def test_inspect_all(self):
-        test_results = list(inspect_all(path=self.tempdir, select=[x.__name__ for x in self.checks]))
+        test_results = list(
+            inspect_all(path=self.tempdir, select=[x.__name__ for x in self.checks], skip_validate=self.skip_validate)
+        )
         true_results = [
             InspectorMessage(
                 message="data is not compressed. Consider enabling compression when writing a dataset.",
@@ -294,7 +338,9 @@ def test_inspect_all_parallel(self):
             self.assertCountEqual(first=test_results, second=true_results)
 
     def test_inspect_nwbfile(self):
-        test_results = list(inspect_nwbfile(nwbfile_path=self.nwbfile_paths[0], checks=self.checks))
+        test_results = list(
+            inspect_nwbfile(nwbfile_path=self.nwbfile_paths[0], checks=self.checks, skip_validate=self.skip_validate)
+        )
         true_results = [
             InspectorMessage(
                 message="data is not compressed. Consider enabling compression when writing a dataset.",
@@ -346,7 +392,10 @@ def test_inspect_nwbfile(self):
     def test_inspect_nwbfile_importance_threshold_as_importance(self):
         test_results = list(
             inspect_nwbfile(
-                nwbfile_path=self.nwbfile_paths[0], checks=self.checks, importance_threshold=Importance.CRITICAL
+                nwbfile_path=self.nwbfile_paths[0],
+                checks=self.checks,
+                importance_threshold=Importance.CRITICAL,
+                skip_validate=self.skip_validate,
             )
         )
         true_results = [
@@ -376,7 +425,12 @@ def test_inspect_nwbfile_importance_threshold_as_importance(self):
 
     def test_inspect_nwbfile_importance_threshold_as_string(self):
         test_results = list(
-            inspect_nwbfile(nwbfile_path=self.nwbfile_paths[0], checks=self.checks, importance_threshold="CRITICAL")
+            inspect_nwbfile(
+                nwbfile_path=self.nwbfile_paths[0],
+                checks=self.checks,
+                importance_threshold="CRITICAL",
+                skip_validate=self.skip_validate,
+            )
         )
         true_results = [
             InspectorMessage(
@@ -408,12 +462,13 @@ def test_command_line_runs_cli_only(self):
         os.system(
             f"nwbinspector {str(self.tempdir)} --overwrite --select check_timestamps_match_first_dimension,"
             "check_data_orientation,check_regular_timestamps,check_small_dataset_compression "
-            "--modules random,math,datetime"
+            "--modules random,math,datetime "
+            "--skip-validate "
             f"> {console_output_file}"
         )
         self.assertLogFileContentsEqual(
             test_file_path=console_output_file,
-            true_file_path=Path(__file__).parent / "true_nwbinspector_default_report.txt",
+            true_file_path=self.true_report_file_path,
             skip_first_newlines=True,
         )
 
@@ -421,12 +476,13 @@ def test_command_line_runs_cli_only_parallel(self):
         console_output_file = self.tempdir / "test_console_output_2.txt"
         os.system(
             f"nwbinspector {str(self.tempdir)} --n-jobs 2 --overwrite --select check_timestamps_match_first_dimension,"
-            "check_data_orientation,check_regular_timestamps,check_small_dataset_compression"
+            "check_data_orientation,check_regular_timestamps,check_small_dataset_compression "
+            "--skip-validate "
             f"> {console_output_file}"
         )
         self.assertLogFileContentsEqual(
             test_file_path=console_output_file,
-            true_file_path=Path(__file__).parent / "true_nwbinspector_default_report.txt",
+            true_file_path=self.true_report_file_path,
             skip_first_newlines=True,
         )
 
@@ -434,7 +490,8 @@ def test_command_line_saves_report(self):
         console_output_file = self.tempdir / "test_console_output_3.txt"
         os.system(
             f"nwbinspector {str(self.nwbfile_paths[0])} "
-            f"--report-file-path {self.tempdir / 'test_nwbinspector_report_1.txt'}"
+            f"--report-file-path {self.tempdir / 'test_nwbinspector_report_1.txt'} "
+            "--skip-validate "
             f"> {console_output_file}"
         )
         self.assertFileExists(path=self.tempdir / "test_nwbinspector_report_1.txt")
@@ -444,14 +501,15 @@ def test_command_line_organizes_levels(self):
         os.system(
             f"nwbinspector {str(self.nwbfile_paths[0])} "
             f"--report-file-path {self.tempdir / 'test_nwbinspector_report_2.txt'} "
-            "--levels importance,check_function_name,file_path"
+            "--levels importance,check_function_name,file_path "
+            "--skip-validate "
             f"> {console_output_file}"
         )
         self.assertFileExists(path=self.tempdir / "test_nwbinspector_report_2.txt")
 
     def test_command_line_runs_saves_json(self):
         json_fpath = self.tempdir / "nwbinspector_results.json"
-        os.system(f"nwbinspector {str(self.nwbfile_paths[0])} --json-file-path {json_fpath}")
+        os.system(f"nwbinspector {str(self.nwbfile_paths[0])} --json-file-path {json_fpath} " f"--skip-validate ")
         self.assertFileExists(path=json_fpath)
 
     def test_command_line_on_directory_matches_file(self):
@@ -459,22 +517,22 @@ def test_command_line_on_directory_matches_file(self):
         os.system(
             f"nwbinspector {str(self.tempdir)} --overwrite --select check_timestamps_match_first_dimension,"
             "check_data_orientation,check_regular_timestamps,check_small_dataset_compression"
-            f" --report-file-path {self.tempdir / 'test_nwbinspector_report_3.txt'}"
+            f" --report-file-path {self.tempdir / 'test_nwbinspector_report_3.txt'} "
+            "--skip-validate "
             f"> {console_output_file}"
         )
         self.assertLogFileContentsEqual(
             test_file_path=self.tempdir / "test_nwbinspector_report_3.txt",
-            true_file_path=Path(__file__).parent / "true_nwbinspector_default_report.txt",
+            true_file_path=self.true_report_file_path,
             skip_first_newlines=True,
         )
 
     def test_iterable_check_function(self):
-        @register_check(importance=Importance.BEST_PRACTICE_VIOLATION, neurodata_type=DynamicTable)
-        def iterable_check_function(table: DynamicTable):
-            for col in table.columns:
-                yield InspectorMessage(message=f"Column: {col.name}")
-
-        test_results = list(inspect_nwbfile(nwbfile_path=self.nwbfile_paths[0], select=["iterable_check_function"]))
+        test_results = list(
+            inspect_nwbfile(
+                nwbfile_path=self.nwbfile_paths[0], select=["iterable_check_function"], skip_validate=self.skip_validate
+            )
+        )
         true_results = [
             InspectorMessage(
                 message="Column: start_time",
@@ -496,7 +554,9 @@ def iterable_check_function(table: DynamicTable):
         self.assertCountEqual(first=test_results, second=true_results)
 
     def test_inspect_nwbfile_manual_iteration(self):
-        generator = inspect_nwbfile(nwbfile_path=self.nwbfile_paths[0], checks=self.checks)
+        generator = inspect_nwbfile(
+            nwbfile_path=self.nwbfile_paths[0], checks=self.checks, skip_validate=self.skip_validate
+        )
         message = next(generator)
         true_result = InspectorMessage(
             message="data is not compressed. Consider enabling compression when writing a dataset.",
@@ -511,7 +571,9 @@ def test_inspect_nwbfile_manual_iteration(self):
         self.assertEqual(message, true_result)
 
     def test_inspect_nwbfile_manual_iteration_stop(self):
-        generator = inspect_nwbfile(nwbfile_path=self.nwbfile_paths[2], checks=self.checks)
+        generator = inspect_nwbfile(
+            nwbfile_path=self.nwbfile_paths[2], checks=self.checks, skip_validate=self.skip_validate
+        )
         with self.assertRaises(expected_exception=StopIteration):
             next(generator)
 
@@ -522,6 +584,7 @@ def test_inspect_nwbfile_dandi_config(self):
                 nwbfile_path=self.nwbfile_paths[0],
                 checks=config_checks,
                 config=load_config(filepath_or_keyword="dandi"),
+                skip_validate=self.skip_validate,
             )
         )
         true_results = [
@@ -581,7 +644,16 @@ def test_inspect_nwbfile_dandi_config(self):
         self.assertCountEqual(first=test_results, second=true_results)
 
 
-class TestDANDIConfig(TestInspector):
+class TestInspectorAPIAndCLIZarr(TestInspectorAPIAndCLIHDF5):
+    BackendIOClass = BACKEND_IO_CLASSES["zarr"]
+    true_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "true_nwbinspector_default_report_zarr.txt"
+    skip_validate = True
+
+
+class TestDANDIConfigHDF5(TestInspectorOnBackend):
+    BackendIOClass = BACKEND_IO_CLASSES["hdf5"]
+    true_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "true_nwbinspector_report_with_dandi_config_hdf5.txt"
+    skip_validate = False
     maxDiff = None
 
     @classmethod
@@ -599,14 +671,15 @@ def setUpClass(cls):
         add_simple_table(nwbfiles[0])
         add_flipped_data_orientation_to_acquisition(nwbfiles[1])
 
-        cls.nwbfile_paths = [str(cls.tempdir / f"testing{j}.nwb") for j in range(num_nwbfiles)]
+        suffix = IO_CLASSES_TO_BACKEND[cls.BackendIOClass]
+        cls.nwbfile_paths = [str(cls.tempdir / f"testing{j}.nwb.{suffix}") for j in range(num_nwbfiles)]
         for nwbfile_path, nwbfile in zip(cls.nwbfile_paths, nwbfiles):
-            with NWBHDF5IO(path=nwbfile_path, mode="w") as io:
+            with cls.BackendIOClass(path=nwbfile_path, mode="w") as io:
                 io.write(nwbfile)
 
     @classmethod
     def tearDownClass(cls):
-        rmtree(cls.tempdir)
+        rmtree(cls.tempdir, ignore_errors=True)
 
     def test_inspect_nwbfile_dandi_config_critical_only_entire_registry(self):
         test_results = list(
@@ -615,6 +688,7 @@ def test_inspect_nwbfile_dandi_config_critical_only_entire_registry(self):
                 checks=available_checks,
                 config=load_config(filepath_or_keyword="dandi"),
                 importance_threshold=Importance.CRITICAL,
+                skip_validate=self.skip_validate,
             )
         )
         true_results = [
@@ -646,6 +720,7 @@ def test_inspect_nwbfile_dandi_config_violation_and_above_entire_registry(self):
                 checks=available_checks,
                 config=load_config(filepath_or_keyword="dandi"),
                 importance_threshold=Importance.BEST_PRACTICE_VIOLATION,
+                skip_validate=self.skip_validate,
             )
         )
         true_results = [
@@ -678,18 +753,27 @@ def test_inspect_nwbfile_dandi_config_critical_only_entire_registry_cli(self):
         console_output_file_path = self.tempdir / "test_console_output.txt"
 
         os.system(
-            f"nwbinspector {str(self.tempdir)} --overwrite --config dandi --threshold BEST_PRACTICE_VIOLATION"
+            f"nwbinspector {str(self.tempdir)} --overwrite --config dandi --threshold BEST_PRACTICE_VIOLATION "
+            f"--skip-validate "
             f"> {console_output_file_path}"
         )
 
         self.assertLogFileContentsEqual(
             test_file_path=console_output_file_path,
-            true_file_path=Path(__file__).parent / "true_nwbinspector_report_with_dandi_config.txt",
+            true_file_path=self.true_report_file_path,
             skip_first_newlines=True,
         )
 
 
-class TestCheckUniqueIdentifiersPass(TestCase):
+class TestDANDIConfigZarr(TestDANDIConfigHDF5):
+    BackendIOClass = BACKEND_IO_CLASSES["zarr"]
+    true_report_file_path = EXPECTED_REPORTS_FOLDER_PATH / "true_nwbinspector_report_with_dandi_config_zarr.txt"
+    skip_validate = True
+
+
+class TestCheckUniqueIdentifiersPassHDF5(TestCase):
+    BackendIOClass = BACKEND_IO_CLASSES["hdf5"]
+    skip_validate = True
     maxDiff = None
 
     @classmethod
@@ -700,20 +784,30 @@ def setUpClass(cls):
         for j in range(num_nwbfiles):
             unique_id_nwbfiles.append(make_minimal_nwbfile())
 
-        cls.unique_id_nwbfile_paths = [str(cls.tempdir / f"unique_id_testing{j}.nwb") for j in range(num_nwbfiles)]
+        suffix = IO_CLASSES_TO_BACKEND[cls.BackendIOClass]
+        cls.unique_id_nwbfile_paths = [
+            str(cls.tempdir / f"unique_id_testing{j}.nwb.{suffix}") for j in range(num_nwbfiles)
+        ]
         for nwbfile_path, nwbfile in zip(cls.unique_id_nwbfile_paths, unique_id_nwbfiles):
-            with NWBHDF5IO(path=nwbfile_path, mode="w") as io:
+            with cls.BackendIOClass(path=nwbfile_path, mode="w") as io:
                 io.write(nwbfile)
 
     @classmethod
     def tearDownClass(cls):
-        rmtree(cls.tempdir)
+        rmtree(cls.tempdir, ignore_errors=True)
 
     def test_check_unique_identifiers_pass(self):
-        assert list(inspect_all(path=self.tempdir, select=["check_data_orientation"])) == []
+        test_message = list(
+            inspect_all(path=self.tempdir, select=["check_data_orientation"], skip_validate=self.skip_validate)
+        )
+        expected_message = []
 
+        assert test_message == expected_message
 
-class TestCheckUniqueIdentifiersFail(TestCase):
+
+class TestCheckUniqueIdentifiersFailHDF5(TestCase):
+    BackendIOClass = BACKEND_IO_CLASSES["hdf5"]
+    skip_validate = True
     maxDiff = None
 
     @classmethod
@@ -730,19 +824,23 @@ def setUpClass(cls):
                 )
             )
 
+        suffix = IO_CLASSES_TO_BACKEND[cls.BackendIOClass]
         cls.non_unique_id_nwbfile_paths = [
-            str(cls.tempdir / f"non_unique_id_testing{j}.nwb") for j in range(num_nwbfiles)
+            str(cls.tempdir / f"non_unique_id_testing{j}.nwb.{suffix}") for j in range(num_nwbfiles)
         ]
         for nwbfile_path, nwbfile in zip(cls.non_unique_id_nwbfile_paths, non_unique_id_nwbfiles):
-            with NWBHDF5IO(path=nwbfile_path, mode="w") as io:
+            with cls.BackendIOClass(path=nwbfile_path, mode="w") as io:
                 io.write(nwbfile)
 
     @classmethod
     def tearDownClass(cls):
-        rmtree(cls.tempdir)
+        rmtree(cls.tempdir, ignore_errors=True)
 
     def test_check_unique_identifiers_fail(self):
-        assert list(inspect_all(path=self.tempdir, select=["check_data_orientation"])) == [
+        test_messages = list(
+            inspect_all(path=self.tempdir, select=["check_data_orientation"], skip_validate=self.skip_validate)
+        )
+        expected_messages = [
             InspectorMessage(
                 message=(
                     "The identifier 'not a unique identifier!' is used across the .nwb files: "
@@ -759,6 +857,16 @@ def test_check_unique_identifiers_fail(self):
             )
         ]
 
+        assert test_messages == expected_messages
+
+
+class TestCheckUniqueIdentifiersPassZarr(TestCheckUniqueIdentifiersPassHDF5):
+    BackendIOClass = BACKEND_IO_CLASSES["zarr"]
+
+
+class TestCheckUniqueIdentifiersFailZarr(TestCheckUniqueIdentifiersFailHDF5):
+    BackendIOClass = BACKEND_IO_CLASSES["zarr"]
+
 
 def test_dandi_config_in_vitro_injection():
     """Test that a subject_id starting with 'protein' excludes meaningless CRITICAL-elevated subject checks."""