diff --git a/tagstudio/src/core/constants.py b/tagstudio/src/core/constants.py
index 48c087fd..291c69c2 100644
--- a/tagstudio/src/core/constants.py
+++ b/tagstudio/src/core/constants.py
@@ -13,3 +13,5 @@
 
 TAG_FAVORITE = 1
 TAG_ARCHIVED = 0
+
+TS_FOLDER_NOINDEX: str = ".ts_noindex"
diff --git a/tagstudio/src/core/library/alchemy/library.py b/tagstudio/src/core/library/alchemy/library.py
index 34267eab..210f58e2 100644
--- a/tagstudio/src/core/library/alchemy/library.py
+++ b/tagstudio/src/core/library/alchemy/library.py
@@ -15,7 +15,6 @@
     and_,
     create_engine,
     delete,
-    exists,
     func,
     or_,
     select,
@@ -34,6 +33,7 @@
     TAG_ARCHIVED,
     TAG_FAVORITE,
     TS_FOLDER_NAME,
+    TS_FOLDER_NOINDEX,
 )
 from ...enums import LibraryPrefs
 from .db import make_tables
@@ -362,6 +362,8 @@ def verify_ts_folders(self, library_dir: Path) -> None:
         if not full_ts_path.exists():
             logger.info("creating library directory", dir=full_ts_path)
             full_ts_path.mkdir(parents=True, exist_ok=True)
+            # create noindex file to ignore the folder
+            (full_ts_path / TS_FOLDER_NOINDEX).touch()
 
     def add_entries(self, items: list[Entry]) -> list[int]:
         """Add multiple Entry records to the Library."""
@@ -389,10 +391,10 @@ def remove_entries(self, entry_ids: list[int]) -> None:
             session.query(Entry).where(Entry.id.in_(entry_ids)).delete()
             session.commit()
 
-    def has_path_entry(self, path: Path) -> bool:
+    def get_path_entry(self, path: Path) -> Entry | None:
         """Check if item with given path is in library already."""
         with Session(self.engine) as session:
-            return session.query(exists().where(Entry.path == path)).scalar()
+            return session.scalar(select(Entry).where(Entry.path == path))
 
     def search_library(
         self,
diff --git a/tagstudio/src/core/utils/refresh_dir.py b/tagstudio/src/core/utils/refresh_dir.py
index 87b734ea..b2c164cd 100644
--- a/tagstudio/src/core/utils/refresh_dir.py
+++ b/tagstudio/src/core/utils/refresh_dir.py
@@ -4,7 +4,7 @@
 from time import time
 
 import structlog
-from src.core.constants import TS_FOLDER_NAME
+from src.core import constants
 from src.core.library import Entry, Library
 
 logger = structlog.get_logger(__name__)
@@ -39,7 +39,11 @@ def save_new_files(self) -> Iterator[int]:
         self.files_not_in_library = []
 
     def refresh_dir(self, lib_path: Path) -> Iterator[int]:
-        """Scan a directory for files, and add those relative filenames to internal variables."""
+        """Scan a directory for changes.
+
+        - Keep track of files which are not in library.
+        - Remove files from library which are in ignored dirs.
+        """
         if self.library.library_dir is None:
             raise ValueError("No library directory set.")
 
@@ -49,24 +53,43 @@ def refresh_dir(self, lib_path: Path) -> Iterator[int]:
         self.files_not_in_library = []
         dir_file_count = 0
 
-        for path in lib_path.glob("**/*"):
-            str_path = str(path)
-            if path.is_dir():
+        for root, _, files in lib_path.walk():
+            if "$RECYCLE.BIN" in str(root).upper():
                 continue
 
-            if "$RECYCLE.BIN" in str_path or TS_FOLDER_NAME in str_path:
+            # - if directory contains file `.ts_noindex` then skip the directory
+            if constants.TS_FOLDER_NOINDEX in files:
+                logger.info("TS Ignore File found, skipping", directory=root)
+                # however check if the ignored files aren't in the library; if so, remove them
+                entries_to_remove = []
+                for file in files:
+                    file_path = root / file
+                    entry_path = file_path.relative_to(lib_path)
+                    if entry := self.library.get_path_entry(entry_path):
+                        entries_to_remove.append(entry.id)
+
+                    # Yield output every 1/30 of a second
+                    if (time() - start_time_loop) > 0.034:
+                        # yield but dont increase the count
+                        yield dir_file_count
+                        start_time_loop = time()
+
+                self.library.remove_entries(entries_to_remove)
                 continue
 
-            dir_file_count += 1
-            relative_path = path.relative_to(lib_path)
-            # TODO - load these in batch somehow
-            if not self.library.has_path_entry(relative_path):
-                self.files_not_in_library.append(relative_path)
+            for file in files:
+                path = root / file
+                dir_file_count += 1
+
+                relative_path = path.relative_to(lib_path)
+                # TODO - load these in batch somehow
+                if not self.library.get_path_entry(relative_path):
+                    self.files_not_in_library.append(relative_path)
 
-            # Yield output every 1/30 of a second
-            if (time() - start_time_loop) > 0.034:
-                yield dir_file_count
-                start_time_loop = time()
+                # Yield output every 1/30 of a second
+                if (time() - start_time_loop) > 0.034:
+                    yield dir_file_count
+                    start_time_loop = time()
 
         end_time_total = time()
         logger.info(
diff --git a/tagstudio/tests/macros/test_refresh_dir.py b/tagstudio/tests/macros/test_refresh_dir.py
index 4655d399..a1c206ef 100644
--- a/tagstudio/tests/macros/test_refresh_dir.py
+++ b/tagstudio/tests/macros/test_refresh_dir.py
@@ -3,6 +3,7 @@
 
 import pytest
 from src.core.enums import LibraryPrefs
+from src.core.library import Entry
 from src.core.utils.refresh_dir import RefreshDirTracker
 
 CWD = pathlib.Path(__file__).parent
@@ -22,3 +23,37 @@ def test_refresh_new_files(library, exclude_mode):
 
     # Then
     assert registry.files_not_in_library == [pathlib.Path("FOO.MD")]
+
+
+@pytest.mark.parametrize("library", [TemporaryDirectory()], indirect=True)
+def test_refresh_removes_noindex_content(library):
+    # Given
+    registry = RefreshDirTracker(library=library)
+
+    # create subdirectory with .ts_noindex file in it
+    (library.library_dir / "subdir").mkdir()
+    (library.library_dir / "subdir" / ".ts_noindex").touch()
+    # add entry into library
+    entry = Entry(
+        path=pathlib.Path("subdir/FOO.MD"),
+        folder=library.folder,
+        fields=library.default_fields,
+    )
+    library.add_entries([entry])
+
+    # create its file in noindex directory
+    (library.library_dir / entry.path).touch()
+    # create another file in the same directory
+    (library.library_dir / "subdir" / "test.txt").touch()
+
+    # add non-ignored entry into library
+    (library.library_dir / "root.txt").touch()
+
+    # When
+    list(registry.refresh_dir(library.library_dir))
+
+    # Then
+    # file in noindex folder should be removed
+    assert not library.get_path_entry(entry.path)
+    # file in index folder should be registered
+    assert registry.files_not_in_library == [pathlib.Path("root.txt")]
diff --git a/tagstudio/tests/test_library.py b/tagstudio/tests/test_library.py
index 81f26690..d7f4cf8a 100644
--- a/tagstudio/tests/test_library.py
+++ b/tagstudio/tests/test_library.py
@@ -18,11 +18,11 @@ def test_library_add_file(library):
         fields=library.default_fields,
     )
 
-    assert not library.has_path_entry(entry.path)
+    assert not library.get_path_entry(entry.path)
 
     assert library.add_entries([entry])
 
-    assert library.has_path_entry(entry.path)
+    assert library.get_path_entry(entry.path) is not None
 
 
 def test_create_tag(library, generate_tag):