diff --git a/bundled/tool/lsp_server.py b/bundled/tool/lsp_server.py
index 5dfd3fe..74bc9fb 100644
--- a/bundled/tool/lsp_server.py
+++ b/bundled/tool/lsp_server.py
@@ -650,9 +650,12 @@ def _run_tool_on_document(
                 cwd=cwd,
                 source=source,
             )
+        except isort.exceptions.FileSkipComment:
+            log_warning(f"Skipping file with 'skip_file' comment: {document.path}")
+            return None
         except isort.exceptions.FileSkipped:
             log_warning(traceback.format_exc(chain=True))
-            # Ignore file skipped.
+            return None
         except Exception:
             log_error(traceback.format_exc(chain=True))
             raise