diff --git a/tests/spec_decode/e2e/test_compatibility.py b/tests/spec_decode/e2e/test_compatibility.py
index 629074188a6c1..af8397c235f48 100644
--- a/tests/spec_decode/e2e/test_compatibility.py
+++ b/tests/spec_decode/e2e/test_compatibility.py
@@ -5,40 +5,6 @@
 from .conftest import get_output_from_llm_generator
 
 
-@pytest.mark.parametrize("common_llm_kwargs", [{
-    "model": "JackFram/llama-68m",
-    "speculative_model": "JackFram/llama-68m",
-    "num_speculative_tokens": 5,
-}])
-@pytest.mark.parametrize("per_test_common_llm_kwargs", [
-    {
-        "enable_chunked_prefill": True,
-    },
-])
-@pytest.mark.parametrize("test_llm_kwargs", [{}])
-@pytest.mark.parametrize("seed", [1])
-def test_spec_decode_xfail_chunked_prefill(test_llm_generator):
-    """Verify that speculative decoding with chunked prefill fails.
-    """
-    output_len = 128
-    temperature = 0.0
-
-    prompts = [
-        "Hello, my name is",
-    ]
-
-    sampling_params = SamplingParams(
-        max_tokens=output_len,
-        ignore_eos=True,
-        temperature=temperature,
-    )
-
-    with pytest.raises(ValueError,
-                       match="Speculative decoding and chunked prefill"):
-        get_output_from_llm_generator(test_llm_generator, prompts,
-                                      sampling_params)
-
-
 @pytest.mark.parametrize("common_llm_kwargs", [{
     "model": "meta-llama/Llama-2-7b-chat-hf",
     "speculative_model": "JackFram/llama-68m",
diff --git a/tests/spec_decode/e2e/test_ngram_correctness.py b/tests/spec_decode/e2e/test_ngram_correctness.py
index a93aca20cd4bf..18a2f37fe784a 100644
--- a/tests/spec_decode/e2e/test_ngram_correctness.py
+++ b/tests/spec_decode/e2e/test_ngram_correctness.py
@@ -49,29 +49,34 @@
         "speculative_model": "[ngram]",
         "num_speculative_tokens": 5,
         "ngram_prompt_lookup_max": 3,
-        "enable_chunked_prefill": False,
     },
     {
         "speculative_model": "[ngram]",
         "num_speculative_tokens": 5,
         "ngram_prompt_lookup_max": 3,
-        "enable_chunked_prefill": True,
-        "speculative_disable_mqa_scorer": True,
-        "max_num_batched_tokens": 4,
-        "max_num_seqs": 4
     },
 ])
 @pytest.mark.parametrize("output_len", [
     256,
 ])
 @pytest.mark.parametrize("batch_size", [1, 32])
+@pytest.mark.parametrize("prefill_chunk_size", [-1, 4])
 @pytest.mark.parametrize("seed", [1])
 def test_ngram_e2e_greedy_correctness(vllm_runner, common_llm_kwargs,
                                       per_test_common_llm_kwargs,
                                       baseline_llm_kwargs, test_llm_kwargs,
                                       batch_size: int, output_len: int,
-                                      seed: int):
+                                      prefill_chunk_size: int, seed: int):
     """Verify greedy equality on a tiny model with different batch size."""
+    if prefill_chunk_size > 0:
+        common_llm_kwargs.update(
+            **{
+                "enable_chunked_prefill": True,
+                "max_num_batched_tokens": prefill_chunk_size,
+                "max_num_seqs": prefill_chunk_size
+            })
+    else:
+        common_llm_kwargs["enable_chunked_prefill"] = True
     run_equality_correctness_test(vllm_runner,
                                   common_llm_kwargs,
                                   per_test_common_llm_kwargs,
diff --git a/tests/spec_decode/test_ngram_worker.py b/tests/spec_decode/test_ngram_worker.py
index 3995f87898afb..f66e957186604 100644
--- a/tests/spec_decode/test_ngram_worker.py
+++ b/tests/spec_decode/test_ngram_worker.py
@@ -118,7 +118,8 @@ def test_ngram_algo_correctness_for_batches_not_match_all():
         num_gpu_blocks,
         block_size,
         final_prompt_lens=final_prompt_lens)
-
+    for sg in seq_group_metadata_list:
+        sg.is_prompt = False
     proposals = proposer.get_spec_proposals(
         execute_model_req=ExecuteModelRequest(
             seq_group_metadata_list=seq_group_metadata_list,
@@ -147,7 +148,7 @@ def test_ngram_algo_correctness_for_batches_not_match_all():
 def test_ngram_algo_correctness_for_batches_match_all():
     """Verify our ngram algo find the right candidate in the prompt
 
-    For the scenario find candidate in all batchs
+    For the scenario find candidate in all batches
     """
 
     block_size = 32
@@ -192,6 +193,10 @@ def test_ngram_algo_correctness_for_batches_match_all():
         block_size,
         final_prompt_lens=final_prompt_lens)
 
+    # Normally drafter is run on decode requests only; here we check the output
+    # of the ngram worker as it is the sole proposer that has no forward.
+    for sg in seq_group_metadata_list:
+        sg.is_prompt = False
     proposals = proposer.get_spec_proposals(
         execute_model_req=ExecuteModelRequest(
             seq_group_metadata_list=seq_group_metadata_list,