diff --git a/libraries/transformer/src/main/java/androidx/media3/transformer/AudioGraphInput.java b/libraries/transformer/src/main/java/androidx/media3/transformer/AudioGraphInput.java
index 160b4703d5..2db5b1b672 100644
--- a/libraries/transformer/src/main/java/androidx/media3/transformer/AudioGraphInput.java
+++ b/libraries/transformer/src/main/java/androidx/media3/transformer/AudioGraphInput.java
@@ -282,6 +282,14 @@ import java.util.concurrent.atomic.AtomicReference;
     if (pendingMediaItemChange.get() != null) {
       return false;
     }
+    if (currentItemExpectedInputDurationUs != C.TIME_UNSET) {
+      // When exporting a sequence of items, we rely on currentItemExpectedInputDurationUs and
+      // receivedEndOfStreamFromInput to determine silence padding.
+      // Use isCurrentItemLast to correctly propagate end of stream once for the entire sequence.
+      return isCurrentItemLast && (receivedEndOfStreamFromInput || queueEndOfStreamAfterSilence);
+    }
+    // For a looping sequence, currentItemExpectedInputDurationUs is unset, and
+    // there isn't a last item -- end of stream is passed through directly.
     return receivedEndOfStreamFromInput || queueEndOfStreamAfterSilence;
   }
 
diff --git a/libraries/transformer/src/main/java/androidx/media3/transformer/SequenceAssetLoader.java b/libraries/transformer/src/main/java/androidx/media3/transformer/SequenceAssetLoader.java
index 14ef0dc0f1..5103f02e71 100644
--- a/libraries/transformer/src/main/java/androidx/media3/transformer/SequenceAssetLoader.java
+++ b/libraries/transformer/src/main/java/androidx/media3/transformer/SequenceAssetLoader.java
@@ -277,7 +277,7 @@ import java.util.concurrent.atomic.AtomicInteger;
       if (wrappedSampleConsumer == null) {
         return null;
       }
-      sampleConsumer = new SampleConsumerWrapper(wrappedSampleConsumer);
+      sampleConsumer = new SampleConsumerWrapper(wrappedSampleConsumer, trackType);
       sampleConsumersByTrackType.put(trackType, sampleConsumer);
 
       if (forceAudioTrack && reportedTrackCount.get() == 1 && trackType == C.TRACK_TYPE_VIDEO) {
@@ -290,7 +290,7 @@ import java.util.concurrent.atomic.AtomicInteger;
                         .setPcmEncoding(C.ENCODING_PCM_16BIT)
                         .build()));
         sampleConsumersByTrackType.put(
-            C.TRACK_TYPE_AUDIO, new SampleConsumerWrapper(wrappedAudioSampleConsumer));
+            C.TRACK_TYPE_AUDIO, new SampleConsumerWrapper(wrappedAudioSampleConsumer, trackType));
       }
     } else {
       // TODO(b/270533049): Remove the check below when implementing blank video frames generation.
@@ -391,13 +391,15 @@ import java.util.concurrent.atomic.AtomicInteger;
   private final class SampleConsumerWrapper implements SampleConsumer {
 
     private final SampleConsumer sampleConsumer;
+    private final @C.TrackType int trackType;
 
     private long totalDurationUs;
     private boolean audioLoopingEnded;
     private boolean videoLoopingEnded;
 
-    public SampleConsumerWrapper(SampleConsumer sampleConsumer) {
+    public SampleConsumerWrapper(SampleConsumer sampleConsumer, @C.TrackType int trackType) {
       this.sampleConsumer = sampleConsumer;
+      this.trackType = trackType;
     }
 
     @Nullable
@@ -426,8 +428,15 @@ import java.util.concurrent.atomic.AtomicInteger;
       if (inputBuffer.isEndOfStream()) {
         nonEndedTrackCount.decrementAndGet();
         if (currentMediaItemIndex < editedMediaItems.size() - 1 || isLooping) {
-          inputBuffer.clear();
-          inputBuffer.timeUs = 0;
+          if (trackType == C.TRACK_TYPE_AUDIO && !isLooping && decodeAudio) {
+            // Trigger silence generation (if needed) for a decoded audio track when end of stream
+            // is first encountered. This helps us avoid a muxer deadlock when audio track is
+            // shorter than video track. Not applicable for looping sequences.
+            checkState(sampleConsumer.queueInputBuffer());
+          } else {
+            inputBuffer.clear();
+            inputBuffer.timeUs = 0;
+          }
           if (nonEndedTrackCount.get() == 0) {
             switchAssetLoader();
           }
diff --git a/libraries/transformer/src/test/java/androidx/media3/transformer/AudioGraphInputTest.java b/libraries/transformer/src/test/java/androidx/media3/transformer/AudioGraphInputTest.java
index f425b37d85..d12b075ed6 100644
--- a/libraries/transformer/src/test/java/androidx/media3/transformer/AudioGraphInputTest.java
+++ b/libraries/transformer/src/test/java/androidx/media3/transformer/AudioGraphInputTest.java
@@ -170,7 +170,100 @@ public class AudioGraphInputTest {
   }
 
   @Test
-  public void isEnded_withEndOfStreamQueued_returnsTrue() throws Exception {
+  public void isEnded_withEndOfStreamQueuedAndItemIsNotLastAndDurationIsSet_returnsFalse()
+      throws Exception {
+    AudioGraphInput audioGraphInput =
+        new AudioGraphInput(
+            /* requestedOutputAudioFormat= */ AudioFormat.NOT_SET,
+            /* editedMediaItem= */ FAKE_ITEM,
+            /* inputFormat= */ getPcmFormat(MONO_44100));
+
+    audioGraphInput.onMediaItemChanged(
+        /* editedMediaItem= */ FAKE_ITEM,
+        /* durationUs= */ 0,
+        /* decodedFormat= */ getPcmFormat(MONO_44100),
+        /* isLast= */ false);
+
+    checkState(!audioGraphInput.getOutput().hasRemaining());
+    assertThat(audioGraphInput.isEnded()).isFalse();
+
+    // Queue EOS.
+    audioGraphInput.getInputBuffer().setFlags(C.BUFFER_FLAG_END_OF_STREAM);
+    checkState(audioGraphInput.queueInputBuffer());
+
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.isEnded()).isFalse();
+  }
+
+  @Test
+  public void isEnded_withEndOfStreamQueuedAndItemIsLastAndDurationIsSet_returnsTrue()
+      throws Exception {
+    AudioGraphInput audioGraphInput =
+        new AudioGraphInput(
+            /* requestedOutputAudioFormat= */ AudioFormat.NOT_SET,
+            /* editedMediaItem= */ FAKE_ITEM,
+            /* inputFormat= */ getPcmFormat(MONO_44100));
+
+    audioGraphInput.onMediaItemChanged(
+        /* editedMediaItem= */ FAKE_ITEM,
+        /* durationUs= */ 0,
+        /* decodedFormat= */ getPcmFormat(MONO_44100),
+        /* isLast= */ true);
+
+    checkState(!audioGraphInput.getOutput().hasRemaining());
+    assertThat(audioGraphInput.isEnded()).isFalse();
+
+    // Queue EOS.
+    audioGraphInput.getInputBuffer().setFlags(C.BUFFER_FLAG_END_OF_STREAM);
+    checkState(audioGraphInput.queueInputBuffer());
+
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    assertThat(audioGraphInput.isEnded()).isTrue();
+  }
+
+  @Test
+  public void isEnded_withEndOfStreamQueuedAndItemIsNotLastAndDurationIsPositive_returnsFalse()
+      throws Exception {
+    AudioGraphInput audioGraphInput =
+        new AudioGraphInput(
+            /* requestedOutputAudioFormat= */ AudioFormat.NOT_SET,
+            /* editedMediaItem= */ FAKE_ITEM,
+            /* inputFormat= */ getPcmFormat(MONO_44100));
+
+    audioGraphInput.onMediaItemChanged(
+        /* editedMediaItem= */ FAKE_ITEM,
+        /* durationUs= */ 500_000,
+        /* decodedFormat= */ getPcmFormat(MONO_44100),
+        /* isLast= */ false);
+
+    checkState(!audioGraphInput.getOutput().hasRemaining());
+    assertThat(audioGraphInput.isEnded()).isFalse();
+
+    // Queue EOS.
+    audioGraphInput.getInputBuffer().setFlags(C.BUFFER_FLAG_END_OF_STREAM);
+    checkState(audioGraphInput.queueInputBuffer());
+
+    // First call to getOutput() triggers silence generation.
+    checkState(!audioGraphInput.getOutput().hasRemaining());
+    int totalBytesOutput = 0;
+    ByteBuffer output;
+    while ((output = audioGraphInput.getOutput()).hasRemaining()) {
+      totalBytesOutput += output.remaining();
+      output.position(output.limit());
+    }
+    assertThat(audioGraphInput.getOutput().hasRemaining()).isFalse();
+    long expectedSampleCount =
+        Util.durationUsToSampleCount(/* durationUs= */ 500_000, MONO_44100.sampleRate);
+    assertThat(totalBytesOutput).isEqualTo(expectedSampleCount * MONO_44100.bytesPerFrame);
+    assertThat(audioGraphInput.isEnded()).isFalse();
+  }
+
+  @Test
+  public void isEnded_withEndOfStreamQueued_whenDurationIsUnset_returnsTrue() throws Exception {
     AudioGraphInput audioGraphInput =
         new AudioGraphInput(
             /* requestedOutputAudioFormat= */ AudioFormat.NOT_SET,
@@ -206,7 +299,7 @@ public class AudioGraphInputTest {
         /* editedMediaItem= */ FAKE_ITEM,
         /* durationUs= */ C.TIME_UNSET,
         /* decodedFormat= */ getPcmFormat(MONO_44100),
-        /* isLast= */ false);
+        /* isLast= */ true);
 
     // Force the media item change to be processed.
     checkState(!audioGraphInput.getOutput().hasRemaining());