diff --git a/keras/src/models/functional.py b/keras/src/models/functional.py
index 613d22083ad4..991b2ec0f8b9 100644
--- a/keras/src/models/functional.py
+++ b/keras/src/models/functional.py
@@ -168,7 +168,7 @@ def call(self, inputs, training=None, mask=None):
         if mask is None:
             masks = [None] * len(inputs)
         else:
-            masks = self._flatten_to_reference_inputs(mask)
+            masks = tree.flatten(mask)
             for x, mask in zip(inputs, masks):
                 if mask is not None:
                     x._keras_mask = mask
@@ -205,8 +205,21 @@ def output_shape(self):
     def _assert_input_compatibility(self, *args):
         return super(Model, self)._assert_input_compatibility(*args)
 
-    def _flatten_to_reference_inputs(self, inputs):
-        return tree.flatten(inputs)
+    def _maybe_warn_inputs_struct_mismatch(self, inputs):
+        try:
+            tree.assert_same_structure(
+                inputs, self._inputs_struct, check_types=False
+            )
+        except:
+            model_inputs_struct = tree.map_structure(
+                lambda x: x.name, self._inputs_struct
+            )
+            inputs_struct = tree.map_structure(lambda x: "*", inputs)
+            warnings.warn(
+                "The structure of `inputs` doesn't match the expected "
+                f"structure: {model_inputs_struct}. "
+                f"Received: the structure of inputs={inputs_struct}"
+            )
 
     def _convert_inputs_to_tensors(self, flat_inputs):
         converted = []
@@ -254,7 +267,8 @@ def _adjust_input_rank(self, flat_inputs):
         return adjusted
 
     def _standardize_inputs(self, inputs):
-        flat_inputs = self._flatten_to_reference_inputs(inputs)
+        self._maybe_warn_inputs_struct_mismatch(inputs)
+        flat_inputs = tree.flatten(inputs)
         flat_inputs = self._convert_inputs_to_tensors(flat_inputs)
         return self._adjust_input_rank(flat_inputs)
 
diff --git a/keras/src/models/functional_test.py b/keras/src/models/functional_test.py
index 553d352ac555..f5cbb229e087 100644
--- a/keras/src/models/functional_test.py
+++ b/keras/src/models/functional_test.py
@@ -1,5 +1,4 @@
 import os
-import warnings
 
 import numpy as np
 import pytest
@@ -162,9 +161,8 @@ def test_input_dict_with_extra_field(self):
 
         model = Functional({"a": input_a}, outputs)
 
-        # Eager call
-        with warnings.catch_warnings():
-            warnings.simplefilter("error")
+        with pytest.warns() as record:
+            # Eager call
             in_val = {
                 "a": np.random.random((2, 3)),
                 "b": np.random.random((2, 1)),
@@ -172,14 +170,17 @@ def test_input_dict_with_extra_field(self):
             out_val = model(in_val)
             self.assertEqual(out_val.shape, (2, 3))
 
-        with warnings.catch_warnings():
-            warnings.simplefilter("error")
             # Symbolic call
             input_a_2 = Input(shape=(3,), batch_size=2)
             input_b_2 = Input(shape=(1,), batch_size=2)
             in_val = {"a": input_a_2, "b": input_b_2}
             out_val = model(in_val)
             self.assertEqual(out_val.shape, (2, 3))
+        self.assertLen(record, 1)
+        self.assertStartsWith(
+            str(record[0].message),
+            r"The structure of `inputs` doesn't match the expected structure:",
+        )
 
     @parameterized.named_parameters(
         ("list", list),
@@ -495,6 +496,20 @@ def compute_output_shape(self, x_shape):
         self.assertAllClose(out, np.ones((2, 2)))
         # Note: it's not intended to work in symbolic mode (yet).
 
+    def test_warning_for_mismatched_inputs_structure(self):
+        i1 = Input((2,))
+        i2 = Input((2,))
+        outputs = layers.Add()([i1, i2])
+        model = Model({"i1": i1, "i2": i2}, outputs)
+
+        with pytest.warns() as record:
+            model([np.ones((2, 2)), np.zeros((2, 2))])
+        self.assertLen(record, 1)
+        self.assertStartsWith(
+            str(record[0].message),
+            r"The structure of `inputs` doesn't match the expected structure:",
+        )
+
     def test_for_functional_in_sequential(self):
         # Test for a v3.4.1 regression.
         if backend.image_data_format() == "channels_first":