diff --git a/flax/nnx/graphlib.py b/flax/nnx/graphlib.py
index a3a0aa8fb..903a415d3 100644
--- a/flax/nnx/graphlib.py
+++ b/flax/nnx/graphlib.py
@@ -2878,9 +2878,21 @@ def pop(
     return states
 
 
-def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> Node:
+def clone(
+  node: Node,
+  variables: bool = True,
+  *,
+  arrays: bool = False,
+  graph: bool | None = None,
+) -> Node:
   """Create a deep copy of the given graph node.
 
+  By default the cloned :class:`Variable` wrappers are new objects but
+  share their underlying ``jax.Array`` buffers with the original. This
+  is cheap, but ``jit(donate_argnums=...)`` will reject the clone
+  because JAX refuses to donate the same buffer twice. Pass
+  ``arrays=True`` to also copy the underlying buffers.
+
   Example usage::
 
     >>> from flax import nnx
@@ -2894,6 +2906,11 @@ def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> N
     node: A graph node object.
     variables: If ``True`` (default) copies of the :class:`Variable` objects are created,
       otherwise the Variables are shared between the original and cloned node.
+    arrays: If ``True``, the underlying ``jax.Array`` buffers of each
+      :class:`Variable` are also copied so the clone has independent
+      memory and is compatible with ``jit(donate_argnums=...)``. Implies
+      ``variables=True``. Defaults to ``False`` (buffers shared with the
+      original).
     graph: If ``True`` (default), uses graph-mode which supports the full
       NNX feature set including shared references. If ``False``, uses
       tree-mode which treats Modules as regular JAX pytrees, avoiding
@@ -2902,6 +2919,9 @@ def clone(node: Node, variables: bool = True, *, graph: bool | None = None) -> N
     A deep copy of the :class:`Module` object.
   """
   graphdef, state = split(node, graph=graph)
+  if arrays:
+    state = jax.tree.map(jax.numpy.copy, state)
+    variables = True
   return merge(graphdef, state, copy=variables)
 
 
diff --git a/tests/nnx/module_test.py b/tests/nnx/module_test.py
index be350e8a9..5421ebdb9 100644
--- a/tests/nnx/module_test.py
+++ b/tests/nnx/module_test.py
@@ -574,6 +574,43 @@ def test_clone(self):
     assert m.b.c.get_value() == m2.b.c.get_value()
     assert m.b.d.get_value() == m2.b.d.get_value()
 
+  def test_clone_arrays_distinct_buffers(self):
+    m = nnx.Linear(in_features=4, out_features=2, rngs=nnx.Rngs(0))
+
+    shared = nnx.clone(m)
+    distinct = nnx.clone(m, arrays=True)
+
+    # Default: buffers shared with the original.
+    assert (
+      m.kernel[...].unsafe_buffer_pointer()
+      == shared.kernel[...].unsafe_buffer_pointer()
+    )
+    # arrays=True: buffers are independent.
+    assert (
+      m.kernel[...].unsafe_buffer_pointer()
+      != distinct.kernel[...].unsafe_buffer_pointer()
+    )
+    # Values still match.
+    np.testing.assert_array_equal(m.kernel[...], distinct.kernel[...])
+
+  def test_clone_arrays_donate_argnums(self):
+    class TestModule(nnx.Module):
+      def __init__(self, rngs):
+        self.linear = nnx.Linear(in_features=4, out_features=2, rngs=rngs)
+        self.linear_copy = nnx.clone(self.linear, arrays=True)
+
+    m = TestModule(nnx.Rngs(0))
+
+    @jax.jit
+    def update(state):
+      return jax.tree.map(lambda x: x + 0.01, state)
+
+    update_donate = jax.jit(update, donate_argnums=(0,))
+    # Pre-fix this raised XlaRuntimeError ("donate the same buffer twice")
+    # because nnx.clone shared the linear and linear_copy buffers.
+    state = update_donate(nnx.state(m))
+    assert state is not None
+
   def test_sow_existing_non_variable_field(self):
     class Foo(nnx.Module):
       def __init__(self) -> None: