diff --git a/tests/v1/spec_decode/test_max_len.py b/tests/v1/spec_decode/test_max_len.py
index bc779f6bd9c4..fa1d0437f7c7 100644
--- a/tests/v1/spec_decode/test_max_len.py
+++ b/tests/v1/spec_decode/test_max_len.py
@@ -7,6 +7,7 @@
 from tests.utils import get_attn_backend_list_based_on_platform
 from vllm import LLM, SamplingParams
 from vllm.platforms import current_platform
+from vllm.sampling_params import StructuredOutputsParams
 
 _PROMPTS = [
     "1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1",
@@ -56,8 +57,34 @@ def test_eagle_max_len(
                 "method": "eagle",
                 "model": "yuhuili/EAGLE-LLaMA3-Instruct-8B",
                 "num_speculative_tokens": num_speculative_tokens,
+                "max_model_len": 80,
             },
-            max_model_len=100,
+            max_model_len=200,
         )
-        sampling_params = SamplingParams(max_tokens=100, ignore_eos=True)
-        llm.generate(_PROMPTS, sampling_params)
+        sampling_params = SamplingParams(max_tokens=200, ignore_eos=True)
+        outputs = llm.generate(_PROMPTS, sampling_params)
+        for o in outputs:
+            assert o.outputs[0].finish_reason == "length", (
+                "This test is only meaningful if the output "
+                "is truncated due to max length"
+            )
+
+        sampling_params = SamplingParams(
+            max_tokens=200,
+            structured_outputs=StructuredOutputsParams(
+                regex="^" + "a b c d e " * 15 + "$"
+            ),
+        )
+        output = llm.generate(_PROMPTS, sampling_params)
+        for o in output:
+            assert o.prompt_token_ids is not None
+            assert (
+                len(o.prompt_token_ids)
+                < 80
+                < len(o.prompt_token_ids) + len(o.outputs[0].token_ids)
+                < 200
+            ), (
+                "This test is only meaningful if the output "
+                "is longer than the eagle max length"
+            )
+            assert o.outputs[0].text == "a b c d e " * 15
diff --git a/vllm/v1/core/sched/scheduler.py b/vllm/v1/core/sched/scheduler.py
index f558306e3b2f..c17b19b58c97 100644
--- a/vllm/v1/core/sched/scheduler.py
+++ b/vllm/v1/core/sched/scheduler.py
@@ -325,6 +325,9 @@ def schedule(self) -> SchedulerOutput:
                     scheduled_spec_decode_tokens[request.request_id] = (
                         request.spec_token_ids
                     )
+                # New spec tokens will be set in `update_draft_token_ids` before the
+                # next step when applicable.
+                request.spec_token_ids = []
 
             # Encoder-related.
             if encoder_inputs_to_schedule:
@@ -1149,10 +1152,7 @@ def update_draft_token_ids(
                 continue
 
             # Add newly generated spec token ids to the request.
-            if not spec_token_ids:
-                # NOTE(woosuk): request.spec_token_ids should be updated.
-                request.spec_token_ids.clear()
-            elif self.structured_output_manager.should_advance(request):
+            if self.structured_output_manager.should_advance(request):
                 metadata = request.structured_output_request
                 request.spec_token_ids = metadata.grammar.validate_tokens(  # type: ignore[union-attr]
                     spec_token_ids
diff --git a/vllm/v1/structured_output/__init__.py b/vllm/v1/structured_output/__init__.py
index acc00526ee89..029129cf1a47 100644
--- a/vllm/v1/structured_output/__init__.py
+++ b/vllm/v1/structured_output/__init__.py
@@ -269,9 +269,10 @@ def grammar_bitmask(
                         and token is not None
                         and not structured_output_request.grammar.is_terminated()
                     ):
-                        assert structured_output_request.grammar.accept_tokens(
+                        accepted = structured_output_request.grammar.accept_tokens(
                             req_id, [token]
                         )
+                        assert accepted, (token, req_id, scheduled_spec_decode_tokens)
                         state_advancements += 1
                     cumulative_index += 1
                 if state_advancements > 0: