diff --git a/rest_api/rest_api/controller/file_upload.py b/rest_api/rest_api/controller/file_upload.py
index f9ca06a45..97b29994e 100644
--- a/rest_api/rest_api/controller/file_upload.py
+++ b/rest_api/rest_api/controller/file_upload.py
@@ -49,10 +49,14 @@ def upload_file(
     additional_params: Optional[str] = Form("null"),  # type: ignore
     fileconverter_params: FileConverterParams = Depends(FileConverterParams.as_form),  # type: ignore
     preprocessor_params: PreprocessorParams = Depends(PreprocessorParams.as_form),  # type: ignore
+    keep_files: Optional[bool] = False,
 ):
     """
     You can use this endpoint to upload a file for indexing
-    (see https://haystack.deepset.ai/guides/rest-api#indexing-documents-in-the-haystack-rest-api-document-store).
+    (see https://docs.haystack.deepset.ai/docs/rest_api#indexing-documents-in-the-haystack-rest-api-documentstore).
+
+    Note: files are removed immediately after being indexed. If you want to keep them, pass the
+    `keep_files=true` parameter in the request payload.
     """
     if not indexing_pipeline:
         raise HTTPException(status_code=501, detail="Indexing Pipeline is not configured.")
@@ -88,3 +92,8 @@ def upload_file(
         params[preprocessor.name] = preprocessor_params.dict()
 
     indexing_pipeline.run(file_paths=file_paths, meta=file_metas, params=params)
+
+    # Clean up indexed files
+    if not keep_files:
+        for p in file_paths:
+            p.unlink()
diff --git a/rest_api/test/test_rest_api.py b/rest_api/test/test_rest_api.py
index e0e7a3b83..ee212bf44 100644
--- a/rest_api/test/test_rest_api.py
+++ b/rest_api/test/test_rest_api.py
@@ -240,11 +240,12 @@ def feedback():
 
 
 @pytest.fixture
-def client():
+def client(tmp_path):
     yaml_pipeline_path = Path(__file__).parent.resolve() / "samples" / "test.haystack-pipeline.yml"
     os.environ["PIPELINE_YAML_PATH"] = str(yaml_pipeline_path)
     os.environ["INDEXING_PIPELINE_NAME"] = "test-indexing"
     os.environ["QUERY_PIPELINE_NAME"] = "test-query"
+    os.environ["FILE_UPLOAD_PATH"] = str(tmp_path)
 
     app = get_app()
     client = TestClient(app)
@@ -324,6 +325,28 @@ def test_file_upload_with_wrong_meta(client):
     MockPDFToTextConverter.mocker.convert.assert_not_called()
 
 
+def test_file_upload_cleanup_after_indexing(client):
+    # mock the upload path to use a dedicated temp folder
+    with mock.patch("rest_api.controller.file_upload.FILE_UPLOAD_PATH", os.environ.get("FILE_UPLOAD_PATH")):
+        file_to_upload = {"files": (Path(__file__).parent / "samples" / "pdf" / "sample_pdf_1.pdf").open("rb")}
+        response = client.post(url="/file-upload", files=file_to_upload, data={})
+        assert 200 == response.status_code
+        # ensure upload folder is empty
+        uploaded_files = os.listdir(os.environ.get("FILE_UPLOAD_PATH"))
+        assert len(uploaded_files) == 0
+
+
+def test_file_upload_keep_files_after_indexing(client):
+    # mock the upload path to use a dedicated temp folder
+    with mock.patch("rest_api.controller.file_upload.FILE_UPLOAD_PATH", os.environ.get("FILE_UPLOAD_PATH")):
+        file_to_upload = {"files": (Path(__file__).parent / "samples" / "pdf" / "sample_pdf_1.pdf").open("rb")}
+        response = client.post(url="/file-upload", files=file_to_upload, params={"keep_files": "true"})
+        assert 200 == response.status_code
+        # ensure original file was kept
+        uploaded_files = os.listdir(os.environ.get("FILE_UPLOAD_PATH"))
+        assert len(uploaded_files) == 1
+
+
 def test_query_with_no_filter(client):
     with mock.patch("rest_api.controller.search.query_pipeline") as mocked_pipeline:
         # `run` must return a dictionary containing a `query` key