diff --git a/gemma/gm/nn/gemma4/_transformer.py b/gemma/gm/nn/gemma4/_transformer.py
index ad7927f2..6da07e93 100644
--- a/gemma/gm/nn/gemma4/_transformer.py
+++ b/gemma/gm/nn/gemma4/_transformer.py
@@ -107,6 +107,64 @@ class _Inputs:
   per_layer_inputs: Float['B L P'] | None = None
 
 
+def compute_valid_audio_soft_token_counts(
+    audio_lengths: Int['B num_clips'], audio_seq_length: int
+) -> Int['B num_clips']:
+  """Compute valid audio soft token counts from raw sample counts."""
+  # frame_length = int(round(16000 * 20.0 / 1000.0)) = 320
+  # hop_length = int(round(16000 * 10.0 / 1000.0)) = 160
+  # frame_size_for_unfold = 321
+  frame_size_for_unfold = 321
+  hop_length = 160
+
+  # Compute mel frames using integer division
+  num_mel_frames = (audio_lengths - frame_size_for_unfold) // hop_length + 1
+  t = num_mel_frames
+  # two 2x downsampling layers
+  for _ in range(2):
+    t_padded = t + 2
+    t = (t_padded - 3) // 2 + 1
+
+  return jnp.minimum(t, audio_seq_length)
+
+
+def mask_padded_audio_tokens(
+    tokens: Int['B L'],
+    inputs_mask: Bool['B L'],
+    valid_counts: Int['B num_clips'],
+    audio_seq_length: int,
+) -> Bool['B L']:
+  """Modify inputs_mask to set padded audio token positions to False."""
+  # audio_mask: [B, L]
+  audio_mask = tokens == _token_utils.AUDIO_SOFT_TOKEN_PLACEHOLDER
+
+  # cumsum: [B, L]
+  cumsum = jnp.cumsum(audio_mask, axis=-1)
+  global_audio_index = (cumsum - 1) * audio_mask
+
+  # clip_idx: [B, L]
+  clip_idx = global_audio_index // audio_seq_length
+  # local_idx: [B, L]
+  local_idx = global_audio_index % audio_seq_length
+
+  # safe_clip_idx: [B, L]
+  safe_clip_idx = jnp.maximum(clip_idx, 0)
+
+  # expanded_valid_counts: [B, L]
+  expanded_valid_counts = jnp.take_along_axis(
+      valid_counts, safe_clip_idx, axis=1
+  )
+
+  # is_valid_audio: [B, L]
+  is_valid_audio = local_idx < expanded_valid_counts
+
+  # padded_audio_mask: [B, L]
+  padded_audio_mask = audio_mask & ~is_valid_audio
+
+  # Modify inputs_mask
+  return inputs_mask & ~padded_audio_mask
+
+
 class Transformer(nn.Module):
   """Base transformer class.
 
@@ -447,6 +505,20 @@ def _encode_and_get_inputs(
         )
 
       inputs_mask = tokens != _PADDING_ID
+      if (
+          audio is not None
+          and audio_lengths is not None
+          and audio_soft_token_counts is not None
+      ):
+        valid_counts = compute_valid_audio_soft_token_counts(
+            audio_lengths, audio_soft_token_counts[0]
+        )
+        inputs_mask = mask_padded_audio_tokens(
+            tokens,
+            inputs_mask,
+            valid_counts,
+            audio_soft_token_counts[0],
+        )
       if positions is None:
         positions = _pos_utils.build_positions_from_mask(inputs_mask)
       if attention_mask is None:
diff --git a/gemma/gm/nn/gemma4/_transformer_test.py b/gemma/gm/nn/gemma4/_transformer_test.py
index 9a6675f6..e0bc9d9d 100644
--- a/gemma/gm/nn/gemma4/_transformer_test.py
+++ b/gemma/gm/nn/gemma4/_transformer_test.py
@@ -16,6 +16,7 @@
 
 from gemma.gm.nn.gemma4 import _gemma4 as gemma4_models
 from gemma.gm.nn.gemma4 import _transformer as gt
+from gemma.gm.vision import _token_utils
 import jax
 import jax.numpy as jnp
 import pytest
@@ -57,3 +58,97 @@ def test_text_only():
   out, params = _get_output(model, tokens=tokens)
   assert 'vision_encoder' not in params
   assert out.logits.shape == (BATCH_SIZE, SEQ_LEN, model.config.num_embed)
+
+
+def test_compute_valid_audio_soft_token_counts():
+  # Test with dummy audio lengths
+  # audio_lengths has shape [B, num_clips]
+  # For 16000 Hz:
+  # 2.0s = 32000 samples.
+  # mel frames = (32000 - 321) // 160 + 1 = 31679 // 160 + 1 = 197 + 1 = 198
+  # mel frames.
+  # Downsampling 1:
+  # t = (198 + 2 - 3) // 2 + 1 = 197 // 2 + 1 = 98 + 1 = 99.
+  # Downsampling 2:
+  # t = (99 + 2 - 3) // 2 + 1 = 98 // 2 + 1 = 49 + 1 = 50.
+  # So for 32000 samples, it should return 50 soft tokens.
+
+  # For 7.5s = 120000 samples.
+  # mel frames = (120000 - 321) // 160 + 1 = 119679 // 160 + 1 = 747 + 1 =
+  # 748 mel frames.
+  # Downsampling 1: (748 + 2 - 3) // 2 + 1 = 373 + 1 = 374.
+  # Downsampling 2: (374 + 2 - 3) // 2 + 1 = 186 + 1 = 187.
+  # So 187 soft tokens.
+
+  audio_lengths = jnp.array([[32000, 120000]], dtype=jnp.int32)
+  counts = gt.compute_valid_audio_soft_token_counts(audio_lengths, 750)
+  assert jnp.array_equal(counts, jnp.array([[50, 187]], dtype=jnp.int32))
+
+
+def test_mask_padded_audio_tokens():
+  # Placeholder token ID is usually _token_utils.AUDIO_SOFT_TOKEN_PLACEHOLDER
+  placeholder = _token_utils.AUDIO_SOFT_TOKEN_PLACEHOLDER
+
+  # tokens has shape [B, L]
+  # B=1, L=13
+  # We have 2 audio clips, max 4 tokens each (so self.audio_seq_length=4)
+  # Clip 0 has valid count 2 (e.g. audio_lengths corresponds to 2 soft tokens)
+  # Clip 1 has valid count 3
+
+  tokens = jnp.array(
+      [[
+          1,
+          2,
+          placeholder,
+          placeholder,
+          placeholder,
+          placeholder,
+          3,
+          4,
+          placeholder,
+          placeholder,
+          placeholder,
+          placeholder,
+          5,
+      ]],
+      dtype=jnp.int32,
+  )
+
+  # inputs_mask initially all True except PAD (none here)
+  inputs_mask = jnp.ones((1, 13), dtype=jnp.bool_)
+
+  # audio_lengths corresponding to [2, 3] soft tokens.
+  audio_lengths = jnp.array([[961, 1601]], dtype=jnp.int32)
+
+  valid_counts = gt.compute_valid_audio_soft_token_counts(
+      audio_lengths, audio_seq_length=4
+  )
+  new_inputs_mask = gt.mask_padded_audio_tokens(
+      tokens, inputs_mask, valid_counts, audio_seq_length=4
+  )
+
+  # Expected mask:
+  # Clip 0 (indices 2..5): first 2 True, last 2 False -> [T, T, F, F]
+  # Clip 1 (indices 8..11): first 3 True, last 1 False -> [T, T, T, F]
+  # Others: True
+  # Expected: [T, T,  T, T, F, F,  T, T,  T, T, T, F,  T]
+  expected_mask = jnp.array(
+      [[
+          True,
+          True,
+          True,
+          True,
+          False,
+          False,
+          True,
+          True,
+          True,
+          True,
+          True,
+          False,
+          True,
+      ]],
+      dtype=jnp.bool_,
+  )
+
+  assert jnp.array_equal(new_inputs_mask, expected_mask)
diff --git a/gemma/gm/text/_gemma4_sampler.py b/gemma/gm/text/_gemma4_sampler.py
index 3fa815d6..66407fb6 100644
--- a/gemma/gm/text/_gemma4_sampler.py
+++ b/gemma/gm/text/_gemma4_sampler.py
@@ -160,23 +160,37 @@ def sample(
       if audio_lengths is None:
         audio_lengths = [len(a) for a in audio]
 
-      for length in audio_lengths:
-        frame_length = int(round(self.audio_sample_rate * 20.0 / 1000.0))
-        hop_length = int(round(self.audio_sample_rate * 10.0 / 1000.0))
-        frame_size_for_unfold = frame_length + 1
-        num_mel_frames = (length - frame_size_for_unfold) // hop_length + 1
-        t = num_mel_frames
+      frame_length = int(round(self.audio_sample_rate * 20.0 / 1000.0))
+      hop_length = int(round(self.audio_sample_rate * 10.0 / 1000.0))
+      frame_size_for_unfold = frame_length + 1
+
+      if self.pad_length is not None:
+        audio_soft_token_counts = [self.audio_seq_length for _ in audio_lengths]
+        t = self.audio_seq_length
         for _ in range(2):
-          t_padded = t + 2
-          t = (t_padded - 3) // 2 + 1
-        audio_soft_token_counts.append(min(t, self.audio_seq_length))
+          t = 2 * t
+        num_mel_frames = t
+        max_audio_len = (
+            (num_mel_frames - 1) * hop_length
+            + frame_size_for_unfold
+            + hop_length
+            - 1
+        )
+      else:
+        for length in audio_lengths:
+          num_mel_frames = (length - frame_size_for_unfold) // hop_length + 1
+          t = num_mel_frames
+          for _ in range(2):
+            t_padded = t + 2
+            t = (t_padded - 3) // 2 + 1
+          audio_soft_token_counts.append(min(t, self.audio_seq_length))
+        max_audio_len = max(len(a) for a in audio)
 
       tokens = _token_utils.add_variable_extra_tokens_for_audio(
           tokens,
           soft_token_counts=audio_soft_token_counts,
       )
 
-      max_audio_len = max(len(a) for a in audio)
       padded_audio = np.zeros((len(audio), max_audio_len), dtype=np.float32)
       for i, a in enumerate(audio):
         padded_audio[i, : len(a)] = a
@@ -217,6 +231,7 @@ def sample(
         audio=audio,
         audio_lengths=audio_lengths,
         audio_soft_token_counts=tuple(audio_soft_token_counts),
+        audio_seq_length=self.audio_seq_length,
     )
 
     if max_new_tokens and max_new_tokens > self.max_out_length:
diff --git a/gemma/gm/text/_prefill.py b/gemma/gm/text/_prefill.py
index 46432e68..bdcf62d9 100644
--- a/gemma/gm/text/_prefill.py
+++ b/gemma/gm/text/_prefill.py
@@ -21,6 +21,8 @@
 from gemma.gm.data import _functional
 from gemma.gm.nn import _config
 from gemma.gm.nn import _transformer_like
+from gemma.gm.nn.gemma4._transformer import compute_valid_audio_soft_token_counts
+from gemma.gm.nn.gemma4._transformer import mask_padded_audio_tokens
 from gemma.gm.text import _sampler_loop
 from gemma.gm.text import _turn_utils
 from gemma.gm.typing import _common
@@ -63,6 +65,7 @@ def prefill(
     audio=None,
     audio_lengths=None,
     audio_soft_token_counts=None,
+    audio_seq_length: int | None = None,
 ) -> _sampler_loop.SamplingState:
   """Pre-fill the KV cache and initial model input.
 
@@ -83,6 +86,7 @@ def prefill(
     audio: Audio input data or None.
     audio_lengths: Lengths of audio inputs or None.
     audio_soft_token_counts: Soft token counts for audio or None.
+    audio_seq_length: Max static audio sequence length.
 
   Returns:
     The initial state for the sampling loop.
@@ -223,12 +227,12 @@ def prefill(
     new_used_cache_length = (
         prev_turns.used_cache_length + input.length_with_mm - 1
     )
-  cache = cache.set_end_index(new_used_cache_length)
+  if audio_seq_length is None and audio_lengths is not None:
+    if hasattr(model, 'config') and hasattr(model.config, 'audio_seq_length'):
+      audio_seq_length = model.config.audio_seq_length
+    else:
+      audio_seq_length = 750
 
-  # TODO(epot): The first token was predicted, so could use this, but would
-  # require to duplicate the logic of `_sample_step`, so leave this for later
-  # The `_sample_loop` will re-start from the last prompt token, so use `-1`
-  # as the first token is re-computed.
   return _make_init_state(
       input=input,
       max_out_length=max_out_length,
@@ -236,6 +240,8 @@ def prefill(
       prev_turns=prev_turns,
       cache=cache,
       rng=rng,
+      audio_lengths=audio_lengths,
+      audio_seq_length=audio_seq_length,
   )
 
 
@@ -247,17 +253,36 @@ def _make_init_state(
     prev_turns: _turn_utils.PrevTurns,
     cache: _cache_helper.Cache,
     rng: PRNGKey,
+    audio_lengths: jax.Array | None = None,
+    audio_seq_length: int | None = None,
 ) -> _sampler_loop.SamplingState:
   """Initial state for the sampling loop."""
 
   # The new last token position is shifted by the prompt length (after MM).
   last_token_pos = input.last_token_pos + prev_turns.last_token_pos
+  if audio_lengths is not None and audio_seq_length is not None:
+    valid_counts = compute_valid_audio_soft_token_counts(
+        audio_lengths, audio_seq_length
+    )
+    padded_counts = jnp.sum(audio_seq_length - valid_counts, axis=-1)
+    last_token_pos = last_token_pos - padded_counts
 
   # Pre-compute the full attention mask for the last step.
   full_attention_mask = _make_full_attention_mask(
       input=input,
       prev_turns=prev_turns,
       cache_length=cache.total_cache_length,
+      audio_lengths=audio_lengths,
+      audio_seq_length=audio_seq_length,
+  )
+
+  jax.debug.print(
+      'PREFILL DEBUG: last_token_pos={pos}, new_used_cache_length={cache_len},'
+      ' mask_sum={mask_sum}, tokens_with_mm_len={tokens_len}',
+      pos=last_token_pos,
+      cache_len=new_used_cache_length,
+      mask_sum=full_attention_mask.sum(axis=-1),
+      tokens_len=input.tokens_with_mm.shape[-1],
   )
 
   return _sampler_loop.SamplingState(
@@ -374,6 +399,8 @@ def _make_full_attention_mask(
     input: _types.Input,  # pylint: disable=redefined-builtin
     prev_turns: _turn_utils.PrevTurns,
     cache_length: int,
+    audio_lengths: jax.Array | None = None,
+    audio_seq_length: int | None = None,
 ):
   """Pre-compute the full attention mask for the full `cache_length`.
 
@@ -404,6 +431,8 @@ def _make_full_attention_mask(
     input: The input tokens.
     prev_turns: The previous turns.
     cache_length: The maximum length of the sequence.
+    audio_lengths: Padded audio lengths.
+    audio_seq_length: Max static audio sequence length.
 
   Returns:
     The full attention mask.
@@ -411,6 +440,17 @@ def _make_full_attention_mask(
   # Mask out the padding tokens.
   full_attention_mask = input.tokens_with_mm != _PADDING_ID
 
+  if audio_lengths is not None and audio_seq_length is not None:
+    valid_counts = compute_valid_audio_soft_token_counts(
+        audio_lengths, audio_seq_length
+    )
+    full_attention_mask = mask_padded_audio_tokens(
+        tokens=input.tokens_with_mm,
+        inputs_mask=full_attention_mask,
+        valid_counts=valid_counts,
+        audio_seq_length=audio_seq_length,
+    )
+
   # Compute the full attention mask across turns.
   if prev_turns:
     full_attention_mask = jnp.concatenate(
diff --git a/gemma/gm/text/_prefill_test.py b/gemma/gm/text/_prefill_test.py
index 5cc921c2..b416b210 100644
--- a/gemma/gm/text/_prefill_test.py
+++ b/gemma/gm/text/_prefill_test.py
@@ -18,7 +18,9 @@
 from gemma.gm.text import _prefill
 from gemma.gm.text import _sampler_loop
 from gemma.gm.text import _turn_utils
+from gemma.gm.utils import _cache_helper
 from gemma.gm.utils import _types
+from gemma.gm.vision import _token_utils
 import jax
 import jax.numpy as jnp
 import numpy as np
@@ -159,3 +161,98 @@ def test_full_attention_mask():
       ],
   )
 
+
+def test_full_attention_mask_with_audio():
+  placeholder = _token_utils.AUDIO_SOFT_TOKEN_PLACEHOLDER
+
+  tokens = jnp.array(
+      [[
+          1,
+          2,
+          placeholder,
+          placeholder,
+          placeholder,
+          placeholder,
+          3,
+          4,
+          placeholder,
+          placeholder,
+          placeholder,
+          placeholder,
+          5,
+      ]],
+      dtype=jnp.int32,
+  )
+
+  input_ = _types.Input(
+      text=tokens,
+      images=None,
+      config=_types.InputConfig(
+          support_images=True,
+          num_tokens_per_image=100,
+          special_tokens=gm.text.Gemma3Tokenizer.special_tokens,
+      ),
+  )
+
+  audio_lengths = jnp.array([[961, 1601]], dtype=jnp.int32)
+
+  mask = _prefill._make_full_attention_mask(
+      input=input_,
+      prev_turns=_turn_utils.PrevTurns(last_state=None),
+      cache_length=20,
+      audio_lengths=audio_lengths,
+      audio_seq_length=4,
+  )
+
+  expected_mask = jnp.array(
+      [[
+          True,
+          True,
+          True,
+          True,
+          False,
+          False,
+          True,
+          True,
+          True,
+          True,
+          True,
+          False,
+          True,
+          True,
+          True,
+          True,
+          True,
+          True,
+          True,
+          True,
+      ]],
+      dtype=jnp.bool_,
+  )
+
+  np.testing.assert_array_equal(mask, expected_mask)
+
+  dummy_cache = _cache_helper.Cache({
+      'layer_0': {
+          'k': jnp.zeros((1, 20, 8, 128)),
+          'v': jnp.zeros((1, 20, 8, 128)),
+          'positions': jnp.zeros((1, 20)),
+          'end_index': jnp.zeros((1,)),
+      }
+  })
+
+  init_state = _prefill._make_init_state(
+      input=input_,
+      max_out_length=10,
+      new_used_cache_length=input_.length_with_mm - 1,
+      prev_turns=_turn_utils.PrevTurns(last_state=None),
+      cache=dummy_cache,
+      rng=jax.random.PRNGKey(0),
+      audio_lengths=audio_lengths,
+      audio_seq_length=4,
+  )
+
+  # The last token position should be 9 (12 - 3 padded audio tokens)
+  assert init_state.last_token_pos == 9
+  # The init cache length should be 12 (13 - 1)
+  assert init_state.init_cache_length == 12