diff --git a/cpp/bench/run.cpp b/cpp/bench/run.cpp
index 98ac18cb29..20291576a0 100644
--- a/cpp/bench/run.cpp
+++ b/cpp/bench/run.cpp
@@ -539,6 +539,58 @@ static void BM_McapWriterFileWriterChunked(benchmark::State& state) {
   std::remove(filename.c_str());
 }
 
+static void BM_McapWriterFileWriterChunkedManyChannels(benchmark::State& state) {
+  // Create a message payload
+  std::array<std::byte, 4 + 13> payload;
+  const uint32_t length = 13;
+  std::memcpy(payload.data(), &length, 4);
+  std::memcpy(payload.data() + 4, "Hello, world!", 13);
+
+  // Create a chunked writer using the ros1 profile
+  mcap::McapWriter writer;
+  auto options = mcap::McapWriterOptions("ros1");
+  options.chunkSize = uint64_t(state.range(0));
+
+  // Open an output file stream and write the file header
+  const std::string filename = TempFilename();
+  assertOk(writer.open(filename, options));
+
+  // Register a Schema record
+  mcap::Schema stdMsgsString("std_msgs/String", "ros1msg", StringSchema);
+  writer.addSchema(stdMsgsString);
+
+  uint16_t channelCount = uint16_t(state.range(1));
+
+  mcap::Channel topic("/chatter", "ros1", stdMsgsString.id);
+  std::vector<uint16_t> channelIds;
+  for (uint16_t i = 0; i < channelCount; ++i) {
+    // Register a Channel record
+    writer.addChannel(topic);
+    channelIds.push_back(topic.id);
+  }
+
+  // Create a message
+  mcap::Message msg;
+  msg.channelId = topic.id;
+  msg.sequence = 0;
+  msg.publishTime = 0;
+  msg.logTime = msg.publishTime;
+  msg.data = payload.data();
+  msg.dataSize = payload.size();
+
+  while (state.KeepRunning()) {
+    for (size_t i = 0; i < WriteIterations; i++) {
+      msg.channelId = channelIds[i % channelCount];
+      (void)writer.write(msg);
+      benchmark::ClobberMemory();
+    }
+  }
+
+  // Finish writing the file and delete it
+  writer.close();
+  std::remove(filename.c_str());
+}
+
 int main(int argc, char* argv[]) {
   benchmark::RegisterBenchmark("BM_CRC32", BM_CRC32)->RangeMultiplier(10)->Range(1, 10000000);
   benchmark::RegisterBenchmark("BM_McapWriterBufferWriterUnchunkedUnindexed",
@@ -619,6 +671,18 @@ int main(int argc, char* argv[]) {
     ->Arg(100000)
     ->Arg(1000000)
     ->Arg(10000000);
+  benchmark::RegisterBenchmark("BM_McapWriterFileWriterChunkedManyChannels",
+                               BM_McapWriterFileWriterChunkedManyChannels)
+    ->Args({mcap::DefaultChunkSize, 1})
+    ->Args({mcap::DefaultChunkSize, 10})
+    ->Args({mcap::DefaultChunkSize, 100})
+    ->Args({mcap::DefaultChunkSize, 1000})
+    ->Args({mcap::DefaultChunkSize, 10000})
+    ->Args({mcap::DefaultChunkSize * 10, 1})
+    ->Args({mcap::DefaultChunkSize * 10, 10})
+    ->Args({mcap::DefaultChunkSize * 10, 100})
+    ->Args({mcap::DefaultChunkSize * 10, 1000})
+    ->Args({mcap::DefaultChunkSize * 10, 10000});
   benchmark::Initialize(&argc, argv);
   benchmark::RunSpecifiedBenchmarks();
 
diff --git a/cpp/mcap/include/mcap/writer.inl b/cpp/mcap/include/mcap/writer.inl
index abbdc1da56..e1eb26461f 100644
--- a/cpp/mcap/include/mcap/writer.inl
+++ b/cpp/mcap/include/mcap/writer.inl
@@ -723,11 +723,18 @@ void McapWriter::writeChunk(IWritable& output, IChunkWriter& chunkData) {
     const uint64_t messageIndexOffset = output.size();
     if (!options_.noMessageIndex) {
       // Write the message index records
-      for (const auto& [channelId, messageIndex] : currentMessageIndex_) {
-        chunkIndexRecord.messageIndexOffsets.emplace(channelId, output.size());
-        write(output, messageIndex);
+      for (auto& [channelId, messageIndex] : currentMessageIndex_) {
+        // currentMessageIndex_ contains entries for every channel ever seen, not just in this
+        // chunk. Only write message index records for channels with messages in this chunk.
+        if (messageIndex.records.size() > 0) {
+          chunkIndexRecord.messageIndexOffsets.emplace(channelId, output.size());
+          write(output, messageIndex);
+          // reset this message index for the next chunk. This allows us to re-use
+          // allocations vs. the alternative strategy of allocating a fresh set of MessageIndex
+          // objects per chunk.
+          messageIndex.records.clear();
+        }
       }
-      currentMessageIndex_.clear();
     }
     const uint64_t messageIndexLength = output.size() - messageIndexOffset;
 
@@ -743,10 +750,17 @@ void McapWriter::writeChunk(IWritable& output, IChunkWriter& chunkData) {
     chunkIndexRecord.uncompressedSize = uncompressedSize;
   } else if (!options_.noMessageIndex) {
     // Write the message index records
-    for (const auto& [channelId, messageIndex] : currentMessageIndex_) {
-      write(output, messageIndex);
+    for (auto& [channelId, messageIndex] : currentMessageIndex_) {
+      // currentMessageIndex_ contains entries for every channel ever seen, not just in this
+      // chunk. Only write message index records for channels with messages in this chunk.
+      if (messageIndex.records.size() > 0) {
+        write(output, messageIndex);
+        // reset this message index for the next chunk. This allows us to re-use
+        // allocations vs. the alternative strategy of allocating a fresh set of MessageIndex
+        // objects per chunk.
+        messageIndex.records.clear();
+      }
     }
-    currentMessageIndex_.clear();
   }
 
   // Reset uncompressedSize and start/end times for the next chunk