diff --git a/ivas_processing_scripts/processing/chains.py b/ivas_processing_scripts/processing/chains.py
index 84f125a1bc767a4536963cea41c7e4e9f754bb80..6ee222dc5a9bfe31fdd8cae9ac14d5ab4495506c 100755
--- a/ivas_processing_scripts/processing/chains.py
+++ b/ivas_processing_scripts/processing/chains.py
@@ -575,12 +575,15 @@ def validate_input_files(cfg: TestConfig):
     # always throw an error for ISM (and MASA) input
     if input_format.startswith("ISM") or input_format.startswith("MASA"):
         frame_alignment = "error"
+        # NOTE: to override this warning for local testing, simply uncomment the below line
+        # this will override the above variable and enable padding for non-aligned files
+        # frame_alignment = "padding"
 
     if frame_alignment == "padding":
         # Create new input directory for padded files
-        output_dir = cfg.output_path / "20ms_aligned_files"
+        aligned_output_dir = cfg.output_path / "20ms_aligned_files"
         try:
-            output_dir.mkdir(exist_ok=False, parents=True)
+            aligned_output_dir.mkdir(exist_ok=False, parents=True)
         except FileExistsError:
             raise ValueError(
                 "Folder for 20ms aligned files already exists. Please move or delete folder"
@@ -639,24 +642,29 @@ def validate_input_files(cfg: TestConfig):
                         samples=True,
                     )
                     # Write padded data to output directory
-                    write(output_dir / item.name, padded_data, fs)
+                    write(aligned_output_dir / item.name, padded_data, fs)
                     # Update audio file path in list
-                    cfg.items_list[i] = output_dir / item.name
+                    cfg.items_list[i] = aligned_output_dir / item.name
                 else:
                     raise ValueError(
                         f"Value of key frame_alignment does not match possible options. Value: {frame_alignment}. Options: 'padding', 'ignore', 'warning', 'error'"
                     )
             else:
                 if frame_alignment == "padding":
-                    copyfile(item, output_dir / item.name)
+                    copyfile(item, aligned_output_dir / item.name)
                     # Update audio file path in list
-                    cfg.items_list[i] = output_dir / item.name
-                else:
-                    pass
+                    cfg.items_list[i] = aligned_output_dir / item.name
 
     if frame_alignment == "padding":
+        # copy over any metadata files
+        [
+            copyfile(f, aligned_output_dir / f.name)
+            for f in list(cfg.input_path.glob("*.csv"))
+            + list(cfg.input_path.glob("*.met"))
+        ]
+
         # Make the output path as the new input path
-        cfg.input_path = output_dir
+        cfg.input_path = aligned_output_dir
 
 
 def clean_outputs(cfg: TestConfig) -> None: