diff --git a/checkpoint/orbax/checkpoint/_src/handlers/base_pytree_checkpoint_handler.py b/checkpoint/orbax/checkpoint/_src/handlers/base_pytree_checkpoint_handler.py
index e00667cbb..ce6f90fb5 100644
--- a/checkpoint/orbax/checkpoint/_src/handlers/base_pytree_checkpoint_handler.py
+++ b/checkpoint/orbax/checkpoint/_src/handlers/base_pytree_checkpoint_handler.py
@@ -1057,6 +1057,12 @@ class TrainState:
           serialized_item, value_metadata_tree
       )
     else:
+      # Deserialize value metadata tree to the same structure as item to allow
+      # for comparison with item that contains rich types.
+      if self._pytree_metadata_options.support_rich_types:
+        value_metadata_tree = tree_utils.deserialize_tree(
+            value_metadata_tree, item
+        )
       # is_empty_or_leaf is necessary here to treat empty nodes (e.g. empty
       # dicts, lists, custom nodes) as leaves, as they do not contain any
       # actual data to be restored, but are needed to maintain the structure.
@@ -1083,12 +1089,11 @@ class TrainState:
         restore_args, self._pytree_metadata_options
     )
 
-    value_metadata_tree_deserialized = tree_utils.deserialize_tree(
-        value_metadata_tree, item
-    )
-    restore_args_deserialized = tree_utils.deserialize_tree(restore_args, item)
-    value_metadata_tree = value_metadata_tree_deserialized
-    restore_args = restore_args_deserialized
+    if not self._pytree_metadata_options.support_rich_types:
+      value_metadata_tree = tree_utils.deserialize_tree(
+          value_metadata_tree, item
+      )
+    restore_args = tree_utils.deserialize_tree(restore_args, item)
 
     param_infos = self._get_param_infos(
         item=value_metadata_tree,
diff --git a/checkpoint/orbax/checkpoint/_src/tree/utils.py b/checkpoint/orbax/checkpoint/_src/tree/utils.py
index 87d4704bf..9a21804b0 100644
--- a/checkpoint/orbax/checkpoint/_src/tree/utils.py
+++ b/checkpoint/orbax/checkpoint/_src/tree/utils.py
@@ -16,6 +16,7 @@
 
 from typing import Any, Callable, Mapping, Optional, Tuple, TypeVar, Union
 
+import flax
 import jax
 import jax.tree_util as jtu
 from orbax.checkpoint._src.arrays import abstract_arrays
@@ -235,10 +236,14 @@ def _reconstruct_from_keypath(keypath, _):
     result = serialized
     for key in keypath:
       key_name = get_key_name(key)
-      if isinstance(key, jax.tree_util.GetAttrKey) and isinstance_of_namedtuple(
-          result
-      ):
-        result = getattr(result, key_name)
+      if isinstance(key, jax.tree_util.GetAttrKey):
+        if isinstance_of_namedtuple(result):
+          result = getattr(result, key_name)
+        elif isinstance(result, flax.struct.PyTreeNode):
+          # Special case to support flax.struct.PyTreeNode
+          result = result.__dict__[key_name]
+        else:
+          result = result[key_name]
       else:
         # Special case to support Pax.
         if not isinstance(result, (list, tuple)) and key_name not in result: