diff --git a/src/osekit/core/base_dataset.py b/src/osekit/core/base_dataset.py
index 3ffeebfb..b983b07c 100644
--- a/src/osekit/core/base_dataset.py
+++ b/src/osekit/core/base_dataset.py
@@ -151,20 +151,28 @@ def folder(self, folder: Path) -> None:
         """
         self._folder = folder
 
-    def move_files(self, folder: Path) -> None:
+    def move_files(self, folder: Path, *, keep_relative_structure: bool = True) -> None:
         """Move the dataset files to the destination folder.
 
         Parameters
         ----------
         folder: Path
             Destination folder in which the dataset files will be moved.
+        keep_relative_structure: bool
+            If True, the relative path from the dataset to the file will be preserved.
+            If False, the files will be moved to ``folder`` regardless of their original
+            relative path to the dataset folder.
 
         """
         for file in tqdm(
             self.files,
             disable=os.getenv("DISABLE_TQDM", "False").lower() in ("true", "1", "t"),
         ):
-            file.move(folder)
+            if not keep_relative_structure:
+                file.move(folder)
+                continue
+            relative_folder = folder / file.path.relative_to(self.folder).parent
+            file.move(relative_folder)
         self._folder = folder
 
     @property
diff --git a/src/osekit/public/project.py b/src/osekit/public/project.py
index a9235ee4..c11dbbf3 100644
--- a/src/osekit/public/project.py
+++ b/src/osekit/public/project.py
@@ -624,7 +624,10 @@ def _sort_dataset(self, dataset: type[DatasetChild]) -> None:
             self._sort_spectro_dataset(dataset)
 
     def _sort_audio_dataset(self, dataset: AudioDataset) -> None:
-        dataset.move_files(self._get_audio_dataset_subpath(dataset))
+        dataset.move_files(
+            self._get_audio_dataset_subpath(dataset),
+            keep_relative_structure=False,
+        )
 
     def _sort_spectro_dataset(self, dataset: SpectroDataset | LTASDataset) -> None:
         raise NotImplementedError
diff --git a/src/osekit/utils/path.py b/src/osekit/utils/path.py
index de14bd82..c02c831f 100644
--- a/src/osekit/utils/path.py
+++ b/src/osekit/utils/path.py
@@ -40,7 +40,8 @@ def move_tree(
             continue
         file_destination = destination / file.parent.relative_to(source)
         file_destination.mkdir(parents=True, exist_ok=True)
-        shutil.move(file, file_destination / file.name)
+        if not (file_destination / file.name).exists():
+            shutil.move(file, file_destination)
     if not any(destination.iterdir()):
         destination.rmdir()
 
diff --git a/tests/test_core_api_base.py b/tests/test_core_api_base.py
index c437afc9..ebce7377 100644
--- a/tests/test_core_api_base.py
+++ b/tests/test_core_api_base.py
@@ -847,7 +847,7 @@ def test_dataset_move(
 
     # Folder should be changed when dataset is moved
     new_destination = tmp_path / "new_destination"
-    dummy_dataset.move_files(new_destination)
+    dummy_dataset.move_files(new_destination, keep_relative_structure=False)
 
     assert new_destination.exists()
     assert new_destination.is_dir()
diff --git a/tests/test_public_api.py b/tests/test_public_api.py
index 613a8ea6..f9ecf5fd 100644
--- a/tests/test_public_api.py
+++ b/tests/test_public_api.py
@@ -1474,6 +1474,13 @@ def test_rename_transform(
 
     names = (first_name, second_name, second_name)  # Tests both renaming and same name
     for old, new in itertools.pairwise(names):
+        files = {}
+        for dataset in project.get_output_by_transform_name(old):
+            files |= {
+                file.path.name: file.path.relative_to(dataset.folder)
+                for file in dataset.files
+            }
+
         project.rename_transform_with_outputs(old, new)
 
         if old != new:
@@ -1499,6 +1506,10 @@ def test_rename_transform(
             == 2
         )
 
+        for dataset in project.get_output_by_transform_name(new):
+            for file in dataset.files:
+                assert file.path.relative_to(dataset.folder) == files[file.path.name]
+
     # RENAME ERRORS
     with pytest.raises(ValueError, match=r"You can't rename the original dataset."):
         project.rename_transform_with_outputs(