diff --git a/package.json b/package.json
index dc69a9e93..63f13a7c4 100644
--- a/package.json
+++ b/package.json
@@ -20,8 +20,6 @@
     "build:mac": "npm run build && npm run build:flask && npm run build:electron:mac",
     "build:linux": "npm run build && npm run build:flask && npm run build:electron:linux",
     "build:flask": "python -m PyInstaller nwb-guide.spec --log-level DEBUG --clean --noconfirm --distpath ./build/flask",
-    "build:flask:spec:base": "pyi-makespec --name nwb-guide --onedir --collect-data jsonschema_specifications --collect-all dandi --collect-all keyrings --collect-all unittest --collect-all nwbinspector --collect-all neuroconv --collect-all pynwb --collect-all hdmf --collect-all hdmf_zarr --collect-all ndx_dandi_icephys --collect-all sklearn --collect-all ci_info ./pyflask/app.py",
-    "build:flask:spec": "npm run build:flask:spec:base && python prepare_pyinstaller_spec.py",
     "build:electron:win": "electron-builder build --win --publish never",
     "build:electron:mac": "electron-builder build --mac --publish never",
     "build:electron:linux": "electron-builder build --linux --publish never",
diff --git a/prepare_pyinstaller_spec.py b/prepare_pyinstaller_spec.py
deleted file mode 100644
index 5c0a36849..000000000
--- a/prepare_pyinstaller_spec.py
+++ /dev/null
@@ -1,43 +0,0 @@
-"""
-Calling `pyi-makespec` regenerates the base spec file, but we need to extend the recursion limit.
-
-This script is run automatically as a part of `npm run build:flask:spec` after the `pyi-makespec` call.
-"""
-
-from pathlib import Path
-
-with open(file=Path(__file__).parent / "nwb-guide.spec", mode="r") as io:
-    lines = io.readlines()
-
-lines.insert(1, "import sys\n")
-lines.insert(2, "from pathlib import Path\n")
-lines.insert(3, "import scipy\n")
-lines.insert(4, "from PyInstaller.utils.hooks import collect_submodules\n")
-lines.insert(5, "\n")
-lines.insert(6, "sys.setrecursionlimit(sys.getrecursionlimit() * 5)\n")
-lines.insert(7, "\n")
-lines.insert(8, "import scipy\n")
-
-hiddenImportIdx = lines.index("hiddenimports = []\n")
-
-lines[hiddenImportIdx] = (
-    "hiddenimports = [ 'email_validator', *collect_submodules('scipy.special.cython_special'), *os.path.join(os.path.dirname(scipy.__file__), '.libs')]\n\n"
-)
-
-
-# Originally this was a separate `npm` command per platform to account for CLI syntax differences between ; and :
-# The spec file is, however, the same across platforms
-data_line_index = lines.index("datas = []\n")
-lines[data_line_index] = "datas = [('./paths.config.json', '.'), ('./package.json', '.')]\n"
-
-# Another platform specific difference is the app.py location
-app_py_line_index, app_py_line = next((index, line) for index, line in enumerate(lines) if "app.py" in line)
-pyflask_start = app_py_line.find("pyflask")  # Can change on certain systems
-injected_app_py_line_base = app_py_line[: (pyflask_start - 1)]
-injected_app_py_line = injected_app_py_line_base + "f\"{Path('pyflask') / 'app.py'}\"],\n"
-lines[app_py_line_index] = injected_app_py_line
-
-with open(file=Path(__file__).parent / "nwb-guide.spec", mode="w") as io:
-    io.writelines(lines)
-
-print("Successfully injected recursion depth extension and json paths!")