diff --git a/src/batdetect2/outputs/formats/base.py b/src/batdetect2/outputs/formats/base.py
index 9b0f012..12c12bd 100644
--- a/src/batdetect2/outputs/formats/base.py
+++ b/src/batdetect2/outputs/formats/base.py
@@ -27,6 +27,10 @@ def make_path_relative(path: PathLike, audio_dir: PathLike) -> Path:
 
         return path.relative_to(audio_dir)
 
+    audio_parts = audio_dir.parts
+    if audio_parts and path.parts[: len(audio_parts)] == audio_parts:
+        return Path(*path.parts[len(audio_parts) :])
+
     return path
 
 
diff --git a/tests/test_outputs/test_base.py b/tests/test_outputs/test_base.py
new file mode 100644
index 0000000..04c490b
--- /dev/null
+++ b/tests/test_outputs/test_base.py
@@ -0,0 +1,21 @@
+from pathlib import Path
+
+from batdetect2.outputs.formats.base import make_path_relative
+
+
+def test_make_path_relative_strips_shared_relative_prefix() -> None:
+    audio_dir = Path("example_data/audio")
+    path = Path("example_data/audio/subdir/clip.wav")
+
+    relative = make_path_relative(path, audio_dir)
+
+    assert relative == Path("subdir/clip.wav")
+
+
+def test_make_path_relative_returns_dot_for_matching_relative_dir() -> None:
+    audio_dir = Path("example_data/audio")
+    path = Path("example_data/audio")
+
+    relative = make_path_relative(path, audio_dir)
+
+    assert relative == Path(".")