diff --git a/src/transformers/models/whisper/generation_whisper.py b/src/transformers/models/whisper/generation_whisper.py
index 91812155c5719b..8012c3c1bbfcfb 100644
--- a/src/transformers/models/whisper/generation_whisper.py
+++ b/src/transformers/models/whisper/generation_whisper.py
@@ -1000,13 +1000,15 @@ def _stack_split_outputs(self, seek_outputs, model_output_type, device, kwargs):
         # Stack back seek_outputs tensors after splitting them with the split_by_batch_index method
         outputs = {}
         for key in seek_outputs[0].keys():
-            if key == "sequences":
+            if key in ["sequences", "beam_indices"]:
                 outputs[key] = torch.stack([v[key] for v in seek_outputs], dim=0).to(device)
-            if key in ["scores", "encoder_attentions", "encoder_hidden_states", "logits"]:
+            elif key in ["scores", "encoder_attentions", "encoder_hidden_states", "logits"]:
                 outputs[key] = tuple(
                     torch.stack([v[key][i] for v in seek_outputs]).to(device) for i in range(len(seek_outputs[0][key]))
                 )
-            if key in ["decoder_attentions", "decoder_hidden_states", "cross_attentions"]:
+            elif key == "sequences_scores":
+                outputs[key] = torch.stack([v[key] for v in seek_outputs], dim=0).to(device)
+            elif key in ["decoder_attentions", "decoder_hidden_states", "cross_attentions"]:
                 outputs[key] = tuple(
                     tuple(
                         torch.stack([v[key][i][j] for v in seek_outputs]).squeeze(1).to(device)
@@ -1014,7 +1016,7 @@ def _stack_split_outputs(self, seek_outputs, model_output_type, device, kwargs):
                     )
                     for i in range(len(seek_outputs[0][key]))
                 )
-            if key == "past_key_values":
+            elif key == "past_key_values":
                 past_key_value_type = kwargs.get("past_key_values")
                 if seek_outputs[0][key] is not None:
                     outputs[key] = tuple(
diff --git a/tests/models/whisper/test_modeling_whisper.py b/tests/models/whisper/test_modeling_whisper.py
index ebc9ce5ec358eb..f7ac2bc12eb252 100644
--- a/tests/models/whisper/test_modeling_whisper.py
+++ b/tests/models/whisper/test_modeling_whisper.py
@@ -529,6 +529,25 @@ def test_inputs_embeds(self):
             with torch.no_grad():
                 model(**inputs)[0]
 
+    def test_beam_search_output(self):
+        config, input_dict = self.model_tester.prepare_config_and_inputs()
+        model = WhisperForConditionalGeneration(config).to(torch_device).eval()
+
+        input_features = input_dict["input_features"]
+
+        # Perform beam search
+        output = model.generate(
+            input_features, num_beams=3, num_return_sequences=3, return_dict_in_generate=True, output_scores=True
+        )
+
+        # Check if beam_indices and sequences_scores are in the output
+        self.assertIn("beam_indices", output, "beam_indices not found in the output")
+        self.assertIn("sequences_scores", output, "sequences_scores not found in the output")
+
+        # Validate the shapes of the beam_indices and sequences_scores
+        self.assertEqual(output.beam_indices.shape[0], input_features.shape[0] * 3)
+        self.assertEqual(output.sequences_scores.shape[0], input_features.shape[0] * 3)
+
     # training is not supported yet
     @unittest.skip(reason="Training is not supported yet")
     def test_training(self):