diff --git a/binding_generator.py b/binding_generator.py
index 8e0ff24eb4..b151a4b110 100644
--- a/binding_generator.py
+++ b/binding_generator.py
@@ -423,7 +423,7 @@ def generate_bindings(api_filepath, use_template_get_node, bits="64", precision=
     generate_engine_classes_bindings(api, target_dir, use_template_get_node)
     generate_utility_functions(api, target_dir)
     if godot_repo != "":
-        generate_compat_includes(godot_repo, target_dir)
+        generate_compat_includes(godot_repo, output_dir, target_dir)
 
 
 CLASS_ALIASES = {
@@ -1567,19 +1567,19 @@ def generate_engine_classes_bindings(api, output_dir, use_template_get_node):
             header_file.write("\n".join(result))
 
 
-def generate_compat_includes(godot_repo: Path, target_dir: Path):
-    file_types_mapping_godot_cpp_gen = map_header_files(target_dir / "include")
+def generate_compat_includes(godot_repo: Path, output_dir: Path, target_dir: Path):
+    file_types_mapping_godot_cpp_gen = map_header_files(output_dir)
     file_types_mapping_godot = map_header_files(godot_repo)
     # Match the headers
     file_types_mapping = match_headers(file_types_mapping_godot_cpp_gen, file_types_mapping_godot)
 
-    include_gen_folder = Path(target_dir) / "include"
     for file_godot_cpp_name, file_godot_names in file_types_mapping.items():
-        header_filename = file_godot_cpp_name.replace("godot_cpp", "godot_compat")
-        header_filepath = include_gen_folder / header_filename
+        header_filepath = file_godot_cpp_name.replace("godot_cpp", "godot_compat")
+        if "gen/include" not in header_filepath:
+            header_filepath = header_filepath.replace("include/", "gen/include/")
         Path(os.path.dirname(header_filepath)).mkdir(parents=True, exist_ok=True)
         result = []
-        snake_header_name = camel_to_snake(header_filename)
+        snake_header_name = camel_to_snake(header_filepath)
         add_header(f"{snake_header_name}.hpp", result)
 
         header_guard = f"GODOT_COMPAT_{os.path.splitext(os.path.basename(header_filepath).upper())[0]}_HPP"
@@ -1594,7 +1594,7 @@ def generate_compat_includes(godot_repo: Path, target_dir: Path):
         result.append(f"#endif")
         result.append("")
         result.append(f"#endif // ! {header_guard}")
-        with header_filepath.open("w+", encoding="utf-8") as header_file:
+        with Path(header_filepath).open("w+", encoding="utf-8") as header_file:
             header_file.write("\n".join(result))
 
 
diff --git a/compat_generator.py b/compat_generator.py
index 6eacc2a8fb..b37eb9c76b 100644
--- a/compat_generator.py
+++ b/compat_generator.py
@@ -45,6 +45,8 @@ def map_header_files(directory):
             dirs.remove("test")
         if "misc" in dirs:
             dirs.remove("misc")
+        if "gdextension" in dirs:
+            dirs.remove("gdextension")
         for file in files:
             if file.endswith(".h") or file.endswith(".hpp"):
                 relative_path = os.path.relpath(root, directory)