diff --git a/rosbag2_cpp/src/rosbag2_cpp/reindexer.cpp b/rosbag2_cpp/src/rosbag2_cpp/reindexer.cpp
index 5ae804074..5bf6b65f6 100644
--- a/rosbag2_cpp/src/rosbag2_cpp/reindexer.cpp
+++ b/rosbag2_cpp/src/rosbag2_cpp/reindexer.cpp
@@ -165,6 +165,8 @@ void Reindexer::aggregate_metadata(
   const rosbag2_storage::StorageOptions & storage_options)
 {
   std::map<std::string, rosbag2_storage::TopicInformation> temp_topic_info;
+  std::chrono::time_point<std::chrono::high_resolution_clock> latest_log_start =
+    std::chrono::time_point<std::chrono::high_resolution_clock>::min();
 
   // In order to most accurately reconstruct the metadata, we need to
   // visit each of the contained relative files files in the bag,
@@ -191,6 +193,14 @@ void Reindexer::aggregate_metadata(
     auto temp_metadata = bag_reader->get_metadata();
     metadata_.storage_identifier = temp_metadata.storage_identifier;
 
+    // try to find the last log for the most complete custom data section
+    if (latest_log_start < temp_metadata.starting_time) {
+      latest_log_start = temp_metadata.starting_time;
+      if (!temp_metadata.custom_data.empty()) {
+        metadata_.custom_data = temp_metadata.custom_data;
+      }
+    }
+
     if (temp_metadata.starting_time < metadata_.starting_time) {
       metadata_.starting_time = temp_metadata.starting_time;
     }
diff --git a/rosbag2_tests/test/rosbag2_tests/test_reindexer.cpp b/rosbag2_tests/test/rosbag2_tests/test_reindexer.cpp
index 4bbc3b9d3..2aa7a84ed 100644
--- a/rosbag2_tests/test/rosbag2_tests/test_reindexer.cpp
+++ b/rosbag2_tests/test/rosbag2_tests/test_reindexer.cpp
@@ -80,6 +80,7 @@ class ReindexTestFixture : public ParametrizedTemporaryDirectoryFixture
       rosbag2_storage::StorageOptions storage_options;
       storage_options.storage_id = GetParam();
       storage_options.uri = root_bag_path_.string();
+      storage_options.custom_data["name"] = "value";
       writer.open(storage_options);
       rosbag2_storage::TopicMetadata topic;
       topic.name = "/test_topic";
@@ -132,6 +133,15 @@ TEST_P(ReindexTestFixture, test_multiple_files) {
   EXPECT_EQ(generated_metadata.storage_identifier, GetParam());
   EXPECT_EQ(generated_metadata.version, target_metadata.version);
 
+  if (GetParam() != "mcap") {
+    // Skip check for mcap storage since it doesn't store serialized metadata in bag directly on
+    // Iron and Humble. Backporting of the relevant #1423 is not possible without updating
+    // mcap vendor package to the v1.1.0 because we have dependencies from the
+    // mcap_reader_->metadataIndexes(); API which became available only in the
+    // https://github.com/foxglove/mcap/pull/902
+    EXPECT_EQ(generated_metadata.custom_data, target_metadata.custom_data);
+  }
+
   for (const auto & gen_rel_path : generated_metadata.relative_file_paths) {
     EXPECT_TRUE(
       std::find(