diff --git a/src/bids/layout/tests/conftest.py b/src/bids/layout/tests/conftest.py
index d5959045..6451f893 100644
--- a/src/bids/layout/tests/conftest.py
+++ b/src/bids/layout/tests/conftest.py
@@ -1,4 +1,5 @@
 from os.path import join
+import shutil
 
 import pytest
 
@@ -101,3 +102,10 @@ def layout_synthetic(tests_dir, request, db_dir):
 def layout_synthetic_nodb(tests_dir, request, db_dir):
     path = tests_dir / 'data' / 'synthetic'
     return BIDSLayout(path, derivatives=True)
+
+
+@pytest.fixture
+def temporary_dataset(tmp_path, tests_dir):
+    path = tests_dir / 'data' / 'ds005'
+    shutil.copytree(path, tmp_path / 'ds005')
+    return tmp_path / 'ds005'
diff --git a/src/bids/layout/tests/test_layout.py b/src/bids/layout/tests/test_layout.py
index c0c7089a..737db4a1 100644
--- a/src/bids/layout/tests/test_layout.py
+++ b/src/bids/layout/tests/test_layout.py
@@ -1170,3 +1170,38 @@ def test_symlinks_in_path(tests_dir, tmp_path):
     os.symlink(src_sub, link_sub)
 
     assert "Subjects: 1 | Sessions: 2 | Runs: 2" in str(BIDSLayout(tmp_path / "7t_trt"))
+
+
+def test_ignore_dotfiles(temporary_dataset):
+    arbitrary_dotfile = temporary_dataset / '.dotfile'
+    ds_store = temporary_dataset / 'sub-01' / '.DS_Store'
+    osx_companion_file = temporary_dataset / '._task-mixedgamblestask_bold.json'
+
+    arbitrary_dotfile.touch()
+    ds_store.touch()
+    osx_companion_file.touch()
+
+    # Default behavior
+    layout = BIDSLayout(temporary_dataset, validate=False)
+    assert str(temporary_dataset / 'dataset_description.json') in layout.files
+    assert str(arbitrary_dotfile) not in layout.files
+    assert str(ds_store) not in layout.files
+    assert str(osx_companion_file) not in layout.files
+
+    # Explicit ignores do not disable dotfile filtering
+    indexer = BIDSLayoutIndexer(ignore=['some_ignore'])
+    layout = BIDSLayout(temporary_dataset, validate=False, indexer=indexer)
+    assert str(temporary_dataset / 'dataset_description.json') in layout.files
+    assert str(arbitrary_dotfile) not in layout.files
+    assert str(ds_store) not in layout.files
+    assert str(osx_companion_file) not in layout.files
+
+
+def test_empty_directory(temporary_dataset):
+    anat = temporary_dataset / 'sub-01' / 'anat'
+    shutil.rmtree(anat)
+    anat.mkdir()
+
+    layout = BIDSLayout(temporary_dataset)
+
+    assert layout.get(subject='01', datatype='anat') == []
diff --git a/src/bids/layout/validation.py b/src/bids/layout/validation.py
index 50732811..cbf4def9 100644
--- a/src/bids/layout/validation.py
+++ b/src/bids/layout/validation.py
@@ -32,9 +32,12 @@
 
 DEFAULT_LOCATIONS_TO_IGNORE = {
     re.compile(r"^/(code|models|sourcedata|stimuli)"),
-    re.compile(r'/\.'),
 }
 
+ALWAYS_IGNORE = (
+    re.compile(r'/\.'),  # dotfiles should never be indexed
+)
+
 def absolute_path_deprecation_warning():
     warnings.warn("The absolute_paths argument will be removed from PyBIDS "
                   "in 0.14. You can easily access the relative path of "
@@ -156,9 +159,11 @@ def _sort_patterns(patterns, root):
 
 def validate_indexing_args(ignore, force_index, root):
     if ignore is None:
-        ignore = list(
-            DEFAULT_LOCATIONS_TO_IGNORE - set(force_index or [])
-        )
+        ignore = DEFAULT_LOCATIONS_TO_IGNORE - set(force_index or [])
+
+    ignore = list(ignore)
+
+    ignore.extend(ALWAYS_IGNORE)
 
     # root has already been validated to be a directory
     ignore = _sort_patterns(ignore, root)