diff --git a/docgen/generate.py b/docgen/generate.py
index c068cf5..f49fdd1 100644
--- a/docgen/generate.py
+++ b/docgen/generate.py
@@ -31,9 +31,16 @@ def collect_headers(input_arg: Path) -> list[tuple[Path, Path]]:
     base_path is used to compute relative output paths.
     """
     if input_arg.is_file():
+        if input_arg.name.endswith('.generated.h'):
+            print(f"Skipping generated header: {input_arg}", file=sys.stderr)
+            return []
         return [(input_arg, input_arg.parent)]
     elif input_arg.is_dir():
-        return [(h, input_arg) for h in sorted(input_arg.rglob('*.h'))]
+        headers = [
+            h for h in sorted(input_arg.rglob('*.h'))
+            if 'Intermediate' not in h.parts and not h.name.endswith('.generated.h')
+        ]
+        return [(h, input_arg) for h in headers]
     else:
         print(f"Error: {input_arg} is not a file or directory", file=sys.stderr)
         return []