diff --git a/rugnux/Rugnux.cpp b/rugnux/Rugnux.cpp
index 9342d875..370858b7 100644
--- a/rugnux/Rugnux.cpp
+++ b/rugnux/Rugnux.cpp
@@ -1709,6 +1709,19 @@ ProcessResult Rugnux::RunPipeline(RugnuxObserver *observer, bool write_output, b
         }
     }
 
+    // When merging is on, the _process.h5 is skipped because the merged reflections are the wanted
+    // output and the per-image file is large. If nothing indexed there are no merged reflections, so
+    // the run would finish successfully having written no file at all. Write one now: the per-image
+    // messages went past while there was no writer, but the end message still carries the per-image
+    // scalars (spot counts, background, resolution estimate) and the dataset metadata - which is what
+    // anyone asking "why did nothing index" needs, and it is small precisely because nothing indexed.
+    if (!writer && full && write_files && !cancelled_ && result.indexing_rate.value_or(0.0f) <= 0.0f) {
+        logger.Warning("No image indexed, so there are no merged reflections to write - writing "
+                       "{}_process.h5 with the per-image analysis instead", config_.output_prefix);
+        writer = std::make_unique<FileWriter>(start_message, /*check_overwrite_at_start=*/true,
+                                              /*trusted_path=*/true);
+    }
+
     if (writer) {
         writer->WriteHDF5(end_msg);
         writer->Finalize();