diff --git a/workers/file_processing/structure_tool_task.py b/workers/file_processing/structure_tool_task.py
index f36e8afff0..8df8603855 100644
--- a/workers/file_processing/structure_tool_task.py
+++ b/workers/file_processing/structure_tool_task.py
@@ -673,9 +673,6 @@ def _write_pipeline_outputs(
             copy_output_path,
         )
 
-        logger.info("Overwriting INFILE with %s output: %s", label, input_file_path)
-        fs.json_dump(path=input_file_path, data=structured_output)
-
         logger.info("Output written successfully to workflow storage")
         return None
     except Exception as e: