diff --git a/haiku/_src/layer_stack.py b/haiku/_src/layer_stack.py
index cc93129a1..a2cd622b6 100644
--- a/haiku/_src/layer_stack.py
+++ b/haiku/_src/layer_stack.py
@@ -89,13 +89,8 @@ def _split_params(
     name_map: LayerStackTransparencyMapping,
 ) -> base.Params:
   """Splits the stacked parameters."""
-
-  def _split(x):
-    return [jnp.squeeze(s, axis=0) for s in jnp.split(x, x.shape[0], axis=0)]
-
   params = {}
   for mod_name, mod_params in stacked_params.items():
-    split_mod_params = {k: _split(v) for k, v in mod_params.items()}
     for i in range(num_layers):
       new_mod_name = name_map.stacked_to_flat(mod_name, i)
       if new_mod_name in params:
@@ -103,8 +98,7 @@ def _split(x):
             f"Found conflicting unstacked module name for {mod_name} at"
             f" {new_mod_name}."
         )
-      params[new_mod_name] = {k: v[i] for k, v in split_mod_params.items()}
-
+      params[new_mod_name] = jax.tree_map(lambda x: x[i], mod_params)  # pylint:disable=cell-var-from-loop
   return params
 
 
@@ -114,32 +108,27 @@ def _stack_params(
     name_map: LayerStackTransparencyMapping,
 ) -> base.Params:
   """Stacks the split parameters."""
-  params = {}
-  make_empty_param_stack = lambda: ([None] * num_layers)
-
+  # Construct a separate tree for each loop iteration, which we will then
+  # multimap over in a call to jnp.stack. This formulation preserves custom
+  # pytree node types.
+  param_trees = [{} for _ in range(num_layers)]
   for mod_name, mod_params in split_params.items():
     stacked_name_idx = name_map.flat_to_stacked(mod_name)
+    # If the transparency map returns None, this param is not part of the stack.
     if stacked_name_idx is None:
       continue
     stacked_mod_name, idx = stacked_name_idx
-    if stacked_mod_name not in params:
-      params[stacked_mod_name] = collections.defaultdict(make_empty_param_stack)
-
+    if stacked_mod_name not in param_trees[idx]:
+      param_trees[idx][stacked_mod_name] = {}
     for k, v in mod_params.items():
-      if params[stacked_mod_name][k][idx] is not None:
+      if k in param_trees[idx][stacked_mod_name]:
         raise ValueError(
             f"Found conflicting values for param {stacked_mod_name}/{k} at"
             f" index {idx}."
         )
-      params[stacked_mod_name][k][idx] = v
-
-  for mod_name, mod_params in params.items():
-    for k, v in mod_params.items():
-      if None in v:
-        raise ValueError(f"Couldn't find all params for {mod_name}/{k}: {v}")
-      mod_params[k] = jnp.stack(v, axis=0)
+      param_trees[idx][stacked_mod_name][k] = v
 
-  return params
+  return jax.tree_map(lambda *args: jnp.stack(args, axis=0), *param_trees)
 
 
 class _LayerStack: