diff --git a/vllm/v1/core/sched/scheduler.py b/vllm/v1/core/sched/scheduler.py
index 0111fd6e7198..3d68e2210fad 100644
--- a/vllm/v1/core/sched/scheduler.py
+++ b/vllm/v1/core/sched/scheduler.py
@@ -42,7 +42,7 @@
 from vllm.v1.core.sched.request_queue import SchedulingPolicy, create_request_queue
 from vllm.v1.core.sched.utils import check_stop, remove_all
 from vllm.v1.engine import EngineCoreEventType, EngineCoreOutput, EngineCoreOutputs
-from vllm.v1.kv_cache_interface import KVCacheConfig
+from vllm.v1.kv_cache_interface import KVCacheConfig, MambaSpec
 from vllm.v1.metrics.perf import ModelMetrics, PerfStats
 from vllm.v1.metrics.stats import (
     PrefixCacheStats,
@@ -220,6 +220,14 @@ def __init__(
         self.use_pp = self.parallel_config.pipeline_parallel_size > 1
         self.use_v2_model_runner = envs.VLLM_USE_V2_MODEL_RUNNER
 
+        def has_mamba_layers(kv_cache_config: KVCacheConfig) -> bool:
+            return any(
+                isinstance(group_spec.kv_cache_spec, MambaSpec)
+                for group_spec in kv_cache_config.kv_cache_groups
+            )
+
+        self.has_mamba_layers = has_mamba_layers(kv_cache_config)
+
         self.perf_metrics: ModelMetrics | None = None
         if self.log_stats and vllm_config.observability_config.enable_mfu_metrics:
             self.perf_metrics = ModelMetrics(vllm_config)
@@ -274,11 +282,22 @@ def schedule(self) -> SchedulerOutput:
                 req_index += 1
                 continue
 
-            num_new_tokens = (
-                request.num_tokens_with_spec
-                + request.num_output_placeholders
-                - request.num_computed_tokens
+            num_tokens_to_compute = (
+                request.num_tokens_with_spec + request.num_output_placeholders
             )
+            # Ensure new tokens for a request in the prefill phase do not contain
+            # speculative tokens, especially in the last prefill chunk. For a hybrid
+            # model, extra speculative tokens would corrupt the generated mamba state.
+            # TODO: This logic does not yet handle resumed requests.
+            if (
+                self.has_mamba_layers
+                and request.num_computed_tokens < request.num_prompt_tokens
+            ):
+                num_tokens_to_compute = min(
+                    num_tokens_to_compute, request.num_prompt_tokens
+                )
+            num_new_tokens = num_tokens_to_compute - request.num_computed_tokens
+
             if 0 < self.scheduler_config.long_prefill_token_threshold < num_new_tokens:
                 num_new_tokens = self.scheduler_config.long_prefill_token_threshold
             num_new_tokens = min(num_new_tokens, token_budget)