diff --git a/examples/audio/process_audio.py b/examples/audio/process_audio.py
index 8657d53ef957..d34461937284 100644
--- a/examples/audio/process_audio.py
+++ b/examples/audio/process_audio.py
@@ -176,6 +176,7 @@ def main(cfg: ProcessConfig) -> ProcessConfig:
             raise RuntimeError('Model does not have a sampler')
 
     if cfg.audio_dir is not None:
+        input_dir = cfg.audio_dir
         filepaths = list(glob.glob(os.path.join(cfg.audio_dir, f"**/*.{cfg.audio_type}"), recursive=True))
     else:
         # get filenames from manifest
@@ -193,6 +194,15 @@ def main(cfg: ProcessConfig) -> ProcessConfig:
                     audio_file = manifest_dir / audio_file
                 filepaths.append(str(audio_file.absolute()))
 
+        # common path for all files
+        common_path = os.path.commonpath(filepaths)
+        if Path(common_path).is_relative_to(manifest_dir):
+            # if all paths are relative to the manifest, use manifest dir as input dir
+            input_dir = manifest_dir
+        else:
+            # use the parent of the common path as input dir
+            input_dir = Path(common_path).parent
+
     if cfg.max_utts is not None:
         # Limit the number of utterances to process
         filepaths = filepaths[: cfg.max_utts]
@@ -238,6 +248,7 @@ def autocast():
                 batch_size=cfg.batch_size,
                 num_workers=cfg.num_workers,
                 input_channel_selector=cfg.input_channel_selector,
+                input_dir=input_dir,
             )
 
     logging.info(f"Finished processing {len(filepaths)} files!")
diff --git a/nemo/collections/audio/models/audio_to_audio.py b/nemo/collections/audio/models/audio_to_audio.py
index 60c16f756f58..57b4c9d48119 100644
--- a/nemo/collections/audio/models/audio_to_audio.py
+++ b/nemo/collections/audio/models/audio_to_audio.py
@@ -332,6 +332,7 @@ def process(
         batch_size: int = 1,
         num_workers: Optional[int] = None,
         input_channel_selector: Optional[ChannelSelectorType] = None,
+        input_dir: Optional[str] = None,
     ) -> List[str]:
         """
         Takes paths to audio files and returns a list of paths to processed
@@ -344,6 +345,7 @@ def process(
             num_workers: Number of workers for the dataloader
             input_channel_selector (int | Iterable[int] | str): select a single channel or a subset of channels from multi-channel audio.
                             If set to `'average'`, it performs averaging across channels. Disabled if set to `None`. Defaults to `None`.
+            input_dir: Optional, directory that contains the input files. If provided, the output directory will mirror the input directory structure.
 
         Returns:
             Paths to processed audio signals.
@@ -413,9 +415,17 @@ def process(
 
                     for example_idx in range(processed_batch.size(0)):
                         # This assumes the data loader is not shuffling files
-                        file_name = os.path.basename(paths2audio_files[file_idx])
+                        if input_dir is not None:
+                            # Make sure the output has the same directory structure as the input
+                            filepath_relative = os.path.relpath(paths2audio_files[file_idx], start=input_dir)
+                        else:
+                            # Input dir is not provided, save files in the output directory
+                            filepath_relative = os.path.basename(paths2audio_files[file_idx])
                         # Prepare output file
-                        output_file = os.path.join(output_dir, f'processed_{file_name}')
+                        output_file = os.path.join(output_dir, filepath_relative)
+                        # Create output dir if necessary
+                        if not os.path.isdir(os.path.dirname(output_file)):
+                            os.makedirs(os.path.dirname(output_file))
                         # Crop the output signal to the actual length
                         output_signal = processed_batch[example_idx, :, : input_length[example_idx]].cpu().numpy()
                         # Write audio