diff --git a/.chronus/changes/revert-wrong-code-2026-3-29-13-46-47.md b/.chronus/changes/revert-wrong-code-2026-3-29-13-46-47.md
new file mode 100644
index 00000000000..49c3d6012e0
--- /dev/null
+++ b/.chronus/changes/revert-wrong-code-2026-3-29-13-46-47.md
@@ -0,0 +1,7 @@
+---
+changeKind: fix
+packages:
+  - "@typespec/http-client-python"
+---
+
+Revert wrong code to avoid overwrite customized code when generation-subdir is set
\ No newline at end of file
diff --git a/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py b/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
index a95b1fd2f27..37657b08b29 100644
--- a/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
+++ b/packages/http-client-python/generator/pygen/codegen/serializers/__init__.py
@@ -183,8 +183,10 @@ def serialize(self) -> None:
                 # When generation-subdir is configured, generated code goes into a subdirectory
                 # (e.g., _generated/). We also need an __init__.py in the parent namespace dir
                 # so that the package is discoverable by find_packages() / pip install.
-                if self.code_model.options.get("generation-subdir"):
-                    root_dir = self.code_model.get_root_dir()
+                root_dir = self.code_model.get_root_dir()
+                if self.code_model.options.get("generation-subdir") and not self.read_file(
+                    root_dir / Path("__init__.py")
+                ):
                     self.write_file(
                         root_dir / Path("__init__.py"),
                         general_serializer.serialize_pkgutil_init_file(),