diff --git a/vllm_gaudi/v1/worker/hpu_model_runner.py b/vllm_gaudi/v1/worker/hpu_model_runner.py
index 4049b09a..ddb64fee 100644
--- a/vllm_gaudi/v1/worker/hpu_model_runner.py
+++ b/vllm_gaudi/v1/worker/hpu_model_runner.py
@@ -3007,19 +3007,24 @@ def execute_model(
 
                 self.event_start = self.profiler.get_timestamp_us()
                 self.profiler.start("internal", "prefill")
-                # Align behavior of incomplete prompt with gpu_model_runner
-                # If logits_indices is smaller than req_id,
-                # add the last token position
+                # NOTE(tianmu-li): Align behavior of incomplete prompt with gpu_model_runner
+                # If logits_indices is smaller than req_id, the last request is a chunked prompt request that
+                # hasn't finished in this step. We add the last token position to logits_indices to ensure
+                # the last token of the chunk is sampled. This sampled token will be discarded later
                 if logits_indices.shape[0] < len(req_id):
-                    if structured_output:
-                        logits_append = torch.tensor([torch.sum(prompt_len) - 1],
-                                                     device=token_ids.device,
-                                                     dtype=torch.int32)
-                        logits_indices = torch.cat([logits_indices, logits_append])
-                    elif self.use_async_scheduling:
-                        # Discard partial prefill logits for async scheduling
+                    if structured_output or self.use_async_scheduling:
+                        # When there are multiple requests in the batch (e.g. self.use_merged_prefill=True),
+                        # the last token position is the sum of all prompt lengths - 1
+                        # This logic also holds when there is only one request in the batch
+                        logits_indices_append = torch.tensor([torch.sum(prompt_len) - 1],
+                                                             device=token_ids.device,
+                                                             dtype=torch.int32)
+                        logits_indices = torch.cat([logits_indices, logits_indices_append])
+                    if self.use_async_scheduling:
+                        # Discard partial prefill logit for async scheduling
                         # Depends on 1 decode token/batch
-                        invalid_req_indices.append(num_decodes + idx)
+                        prefill_start_idx = num_decodes
+                        invalid_req_indices.append(prefill_start_idx + idx)
                 htorch.core.mark_step()
                 non_flattened_hidden_states, aux_hidden_states, \
                     sample_hidden_states, logits_device = \
@@ -3321,7 +3326,7 @@ def execute_model(
             return AsyncHPUModelRunnerOutput(
                 model_runner_output=model_runner_output,
                 sampled_token_ids=sampled_token_ids,
-                invalid_req_indices=[],
+                invalid_req_indices=invalid_req_indices,
                 async_output_copy_stream=self.async_output_copy_stream,
             )
         model_runner_output = ModelRunnerOutput(