diff --git a/go/cli/mcap/cmd/filter_test.go b/go/cli/mcap/cmd/filter_test.go
index 0b902c141e..314eb50869 100644
--- a/go/cli/mcap/cmd/filter_test.go
+++ b/go/cli/mcap/cmd/filter_test.go
@@ -304,9 +304,9 @@ func TestRecover(t *testing.T) {
 		assert.Equal(t, 0, attachmentCounter)
 		assert.Equal(t, 0, metadataCounter)
 		assert.InDeltaMapValues(t, map[uint16]int{
-			1: 87,
-			2: 87,
-			3: 87,
+			1: 88,
+			2: 88,
+			3: 88,
 		}, messageCounter, 0.0)
 	})
 
diff --git a/go/mcap/mcap.go b/go/mcap/mcap.go
index a8a04e88f1..04587198ad 100644
--- a/go/mcap/mcap.go
+++ b/go/mcap/mcap.go
@@ -166,6 +166,10 @@ func (idx *MessageIndex) Reset() {
 	idx.currentIndex = 0
 }
 
+func (idx *MessageIndex) IsEmpty() bool {
+	return idx.currentIndex == 0
+}
+
 // Entries lists the entries in the message index.
 func (idx *MessageIndex) Entries() []MessageIndexEntry {
 	return idx.Records[:idx.currentIndex]
diff --git a/go/mcap/version.go b/go/mcap/version.go
index c731b8e9a4..e5eb06b4a7 100644
--- a/go/mcap/version.go
+++ b/go/mcap/version.go
@@ -1,4 +1,4 @@
 package mcap
 
 // Version of the MCAP library.
-var Version = "v1.0.0"
+var Version = "v1.0.1"
diff --git a/go/mcap/writer.go b/go/mcap/writer.go
index a8b9f372f9..4a9f0ffa0e 100644
--- a/go/mcap/writer.go
+++ b/go/mcap/writer.go
@@ -463,7 +463,8 @@ func (w *Writer) flushActiveChunk() error {
 	messageIndexOffsets := make(map[uint16]uint64)
 	if !w.opts.SkipMessageIndexing {
 		for _, chanID := range w.channelIDs {
-			if messageIndex, ok := w.messageIndexes[chanID]; ok {
+			messageIndex, ok := w.messageIndexes[chanID]
+			if ok && !messageIndex.IsEmpty() {
 				messageIndexOffsets[messageIndex.ChannelID] = w.w.Size()
 				err = w.WriteMessageIndex(messageIndex)
 				if err != nil {
diff --git a/go/mcap/writer_test.go b/go/mcap/writer_test.go
index bfc33e54a9..e105b8ae46 100644
--- a/go/mcap/writer_test.go
+++ b/go/mcap/writer_test.go
@@ -150,6 +150,7 @@ func TestChunkedReadWrite(t *testing.T) {
 			buf := &bytes.Buffer{}
 			w, err := NewWriter(buf, &WriterOptions{
 				Chunked:         true,
+				ChunkSize:       1,
 				Compression:     compression,
 				IncludeCRC:      true,
 				OverrideLibrary: true,
@@ -174,6 +175,12 @@ func TestChunkedReadWrite(t *testing.T) {
 					"callerid": "100", // cspell:disable-line
 				},
 			}))
+			assert.Nil(t, w.WriteChannel(&Channel{
+				ID:              2,
+				Topic:           "/test2",
+				MessageEncoding: "ros1",
+				SchemaID:        1,
+			}))
 			assert.Nil(t, w.WriteMessage(&Message{
 				ChannelID:   1,
 				Sequence:    0,
@@ -186,13 +193,25 @@ func TestChunkedReadWrite(t *testing.T) {
 					4,
 				},
 			}))
+			assert.Nil(t, w.WriteMessage(&Message{
+				ChannelID:   2,
+				Sequence:    0,
+				LogTime:     100,
+				PublishTime: 100,
+				Data: []byte{
+					1,
+					2,
+					3,
+					4,
+				},
+			}))
 			assert.Nil(t, w.Close())
-			assert.Equal(t, 1, len(w.ChunkIndexes))
+			assert.Equal(t, 2, len(w.ChunkIndexes))
 			assert.Equal(t, 0, len(w.AttachmentIndexes))
-			assert.Equal(t, uint64(1), w.Statistics.MessageCount)
+			assert.Equal(t, uint64(2), w.Statistics.MessageCount)
 			assert.Equal(t, uint32(0), w.Statistics.AttachmentCount)
-			assert.Equal(t, uint32(1), w.Statistics.ChannelCount)
-			assert.Equal(t, uint32(1), w.Statistics.ChunkCount)
+			assert.Equal(t, uint32(2), w.Statistics.ChannelCount)
+			assert.Equal(t, uint32(2), w.Statistics.ChunkCount)
 			assert.Equal(t, int(w.Offset()), buf.Len())
 			lexer, err := NewLexer(buf)
 			assert.Nil(t, err)
@@ -201,13 +220,20 @@ func TestChunkedReadWrite(t *testing.T) {
 				TokenHeader,
 				TokenSchema,
 				TokenChannel,
+				TokenChannel,
+				TokenMessage,
+				// Note: one message index per chunk, meaning that message indices for channels
+				// not present in the chunk are not written.
+				TokenMessageIndex,
 				TokenMessage,
 				TokenMessageIndex,
 				TokenDataEnd,
 				TokenSchema,
 				TokenChannel,
+				TokenChannel,
 				TokenStatistics,
 				TokenChunkIndex,
+				TokenChunkIndex,
 				TokenSummaryOffset,
 				TokenSummaryOffset,
 				TokenSummaryOffset,