diff --git a/docs/examples/example_mitgcm.py b/docs/examples/example_mitgcm.py
index 6a7542fe56..f0f6a62c6c 100644
--- a/docs/examples/example_mitgcm.py
+++ b/docs/examples/example_mitgcm.py
@@ -1,4 +1,6 @@
 from datetime import timedelta
+from pathlib import Path
+from typing import Literal
 
 import numpy as np
 import parcels
@@ -7,7 +9,7 @@
 ptype = {"scipy": parcels.ScipyParticle, "jit": parcels.JITParticle}
 
 
-def run_mitgcm_zonally_reentrant(mode):
+def run_mitgcm_zonally_reentrant(mode: Literal["scipy", "jit"], path: Path):
     """Function that shows how to load MITgcm data in a zonally periodic domain."""
     data_folder = parcels.download_example_dataset("MITgcm_example_data")
     filenames = {
@@ -41,7 +43,7 @@ def periodicBC(particle, fieldset, time):
         size=10,
     )
     pfile = parcels.ParticleFile(
-        "MIT_particles_" + str(mode) + ".zarr",
+        str(path),
         pset,
         outputdt=timedelta(days=1),
         chunks=(len(pset), 1),
@@ -52,12 +54,15 @@ def periodicBC(particle, fieldset, time):
     )
 
 
-def test_mitgcm_output_compare():
-    run_mitgcm_zonally_reentrant("scipy")
-    run_mitgcm_zonally_reentrant("jit")
+def test_mitgcm_output_compare(tmpdir):
+    def get_path(mode: Literal["scipy", "jit"]) -> Path:
+        return tmpdir / f"MIT_particles_{mode}.zarr"
 
-    ds_jit = xr.open_zarr("MIT_particles_jit.zarr")
-    ds_scipy = xr.open_zarr("MIT_particles_scipy.zarr")
+    for mode in ["scipy", "jit"]:
+        run_mitgcm_zonally_reentrant(mode, get_path(mode))
+
+    ds_jit = xr.open_zarr(get_path("jit"))
+    ds_scipy = xr.open_zarr(get_path("scipy"))
 
     np.testing.assert_allclose(ds_jit.lat.data, ds_scipy.lat.data)
     np.testing.assert_allclose(ds_jit.lon.data, ds_scipy.lon.data)
diff --git a/tests/test_examples.py b/tests/test_examples.py
index 30bbd58355..de42fbb86f 100644
--- a/tests/test_examples.py
+++ b/tests/test_examples.py
@@ -1,5 +1,8 @@
+import os
 import runpy
+import shutil
 import sys
+import time
 from pathlib import Path
 
 import pytest
@@ -8,6 +11,33 @@
 example_fnames = [path.name for path in example_folder.glob("*.py")]
 
 
+@pytest.fixture(autouse=True)
+def cleanup_generated_data_files():
+    """Clean up generated data files from test run.
+
+    Records current folder contents before test, and cleans up any generated `.nc` files
+    and `.zarr` folders afterwards. For safety this is non-recursive. This function is
+    only necessary as the scripts being run aren't native pytest tests, so they don't
+    have access to the `tmpdir` fixture.
+
+    """
+    folder_contents = os.listdir()
+    yield
+    time.sleep(0.1)  # Buffer so that files are closed before we try to delete them.
+    for fname in os.listdir():
+        if fname in folder_contents:
+            continue
+        if not (fname.endswith(".nc") or fname.endswith(".zarr")):
+            continue
+
+        path = Path(fname)
+        if path.is_dir():
+            shutil.rmtree(path)
+        else:
+            path.unlink()
+        print(f"Removed {path}")
+
+
 @pytest.mark.parametrize("example_fname", example_fnames)
 def test_example_script(example_fname):
     script = str(example_folder / example_fname)