diff --git a/src/transformers/modeling_utils.py b/src/transformers/modeling_utils.py
index 3247c323685815..7e5d3e54e619e8 100644
--- a/src/transformers/modeling_utils.py
+++ b/src/transformers/modeling_utils.py
@@ -2955,6 +2955,18 @@ def from_pretrained(
                 **kwargs,
             )
         else:
+            # In case one passes a config to `from_pretrained` + "attn_implementation"
+            # override the `_attn_implementation` attribute to `attn_implementation` of the kwargs
+            # Please see: https://github.com/huggingface/transformers/issues/28038
+
+            # Overwrite `config._attn_implementation` by the one from the kwargs --> in auto-factory
+            # we pop attn_implementation from the kwargs but this handles the case where users
+            # passes manually the config to `from_pretrained`.
+            config = copy.deepcopy(config)
+
+            kwarg_attn_imp = kwargs.pop("attn_implementation", None)
+            if kwarg_attn_imp is not None and config._attn_implementation != kwarg_attn_imp:
+                config._attn_implementation = kwarg_attn_imp
             model_kwargs = kwargs
 
         quantizer = None
diff --git a/tests/test_modeling_utils.py b/tests/test_modeling_utils.py
index ddfaad5214dc50..a8a483b4017c84 100755
--- a/tests/test_modeling_utils.py
+++ b/tests/test_modeling_utils.py
@@ -1823,6 +1823,16 @@ def test_error_no_flash_available(self):
 
         self.assertTrue("does not support Flash Attention 2.0" in str(cm.exception))
 
+    def test_error_no_flash_available_with_config(self):
+        with self.assertRaises(ValueError) as cm:
+            config = AutoConfig.from_pretrained("hf-tiny-model-private/tiny-random-MCTCTModel")
+
+            _ = AutoModel.from_pretrained(
+                "hf-tiny-model-private/tiny-random-MCTCTModel", config=config, attn_implementation="flash_attention_2"
+            )
+
+        self.assertTrue("does not support Flash Attention 2.0" in str(cm.exception))
+
     def test_error_wrong_attn_implementation(self):
         with self.assertRaises(ValueError) as cm:
             _ = AutoModel.from_pretrained("hf-tiny-model-private/tiny-random-MCTCTModel", attn_implementation="foo")
@@ -1840,6 +1850,21 @@ def test_not_available_flash(self):
 
         self.assertTrue("the package flash_attn seems to be not installed" in str(cm.exception))
 
+    def test_not_available_flash_with_config(self):
+        if is_flash_attn_2_available():
+            self.skipTest("Please uninstall flash-attn package to run test_not_available_flash")
+
+        config = AutoConfig.from_pretrained("hf-internal-testing/tiny-random-GPTBigCodeModel")
+
+        with self.assertRaises(ImportError) as cm:
+            _ = AutoModel.from_pretrained(
+                "hf-internal-testing/tiny-random-GPTBigCodeModel",
+                config=config,
+                attn_implementation="flash_attention_2",
+            )
+
+        self.assertTrue("the package flash_attn seems to be not installed" in str(cm.exception))
+
     def test_not_available_sdpa(self):
         if is_torch_sdpa_available():
             self.skipTest("This test requires torch<=2.0")