diff --git a/optimum/onnxruntime/modeling_seq2seq.py b/optimum/onnxruntime/modeling_seq2seq.py
index 53abf43e01..7248be4e37 100644
--- a/optimum/onnxruntime/modeling_seq2seq.py
+++ b/optimum/onnxruntime/modeling_seq2seq.py
@@ -33,7 +33,8 @@
     AutoModelForSpeechSeq2Seq,
     AutoModelForVision2Seq,
     GenerationConfig,
-    Pix2StructForConditionalGeneration,  # Pix2struct does not support AutoModel
+    Pix2StructForConditionalGeneration,
+    WhisperForConditionalGeneration,
 )
 from transformers.file_utils import add_end_docstrings, add_start_docstrings_to_model_forward
 from transformers.modeling_outputs import BaseModelOutput, Seq2SeqLMOutput
@@ -1281,7 +1282,6 @@ def get_encoder(self) -> ORTEncoder:
     # Copied from transformers.models.bart.modeling_bart.BartForConditionalGeneration._reorder_cache
     @staticmethod
     def _reorder_cache(past, beam_idx) -> Tuple[Tuple[torch.FloatTensor]]:
-        print("REORDER CACHE CALLED")
         reordered_past = ()
         for layer_past in past:
             # Cached cross_attention states don't have to be reordered -> they are always the same
@@ -1381,51 +1381,27 @@ def prepare_inputs_for_generation(
         self,
         decoder_input_ids,
         past_key_values=None,
+        attention_mask=None,
+        head_mask=None,
+        decoder_head_mask=None,
+        cross_attn_head_mask=None,
         use_cache=None,
         encoder_outputs=None,
-        attention_mask=None,
-        decoder_attention_mask=None,
-        cache_position=None,
         **kwargs,
     ):
-        decoder_position_ids = None
-        if decoder_attention_mask is not None:
-            decoder_position_ids = (decoder_attention_mask.cumsum(-1) - 1).clamp(min=0)
-
-        past_length = 0
+        # cut decoder_input_ids if past is used
         if past_key_values is not None:
-            if isinstance(past_key_values, EncoderDecoderCache):
-                past_length = cache_position[0] if cache_position is not None else past_key_values.get_seq_length()
-            else:
-                past_length = past_key_values[0][0].shape[2]
-
-            # Some generation methods already pass only the last input ID
-            if decoder_input_ids.shape[1] > past_length:
-                remove_prefix_length = past_length
-            else:
-                # Default to old behavior: keep only final ID
-                remove_prefix_length = decoder_input_ids.shape[1] - 1
-
-            decoder_input_ids = decoder_input_ids[:, remove_prefix_length:]
-
-            if decoder_position_ids is not None and decoder_position_ids.shape[1] > decoder_input_ids.shape[1]:
-                decoder_position_ids = decoder_position_ids[:, remove_prefix_length:]
-
-        if cache_position is None:
-            cache_position = torch.arange(
-                past_length, past_length + decoder_input_ids.shape[1], device=decoder_input_ids.device
-            )
-        elif use_cache:
-            cache_position = cache_position[-decoder_input_ids.shape[1] :]
+            decoder_input_ids = decoder_input_ids[:, -1:]
 
         return {
             "encoder_outputs": encoder_outputs,
             "past_key_values": past_key_values,
             "decoder_input_ids": decoder_input_ids,
+            "attention_mask": attention_mask,
+            "head_mask": head_mask,
+            "decoder_head_mask": decoder_head_mask,
+            "cross_attn_head_mask": cross_attn_head_mask,
             "use_cache": use_cache,
-            "decoder_attention_mask": decoder_attention_mask,
-            "decoder_position_ids": decoder_position_ids,
-            "cache_position": cache_position,
         }
 
     def get_encoder(self) -> ORTEncoder:
@@ -1460,6 +1436,9 @@ class _ORTModelForWhisper(WhisperGenerationMixin, ORTModelForSpeechSeq2Seq):
     Whisper implements its own generate() method.
     """
 
+    auto_model_class = WhisperForConditionalGeneration
+    prepare_inputs_for_generation = WhisperForConditionalGeneration.prepare_inputs_for_generation
+
     @classmethod
     def _from_pretrained(
         cls,