diff --git a/lib/galaxy/jobs/command_factory.py b/lib/galaxy/jobs/command_factory.py
index 1ca1bc0ee20..10b9c137347 100644
--- a/lib/galaxy/jobs/command_factory.py
+++ b/lib/galaxy/jobs/command_factory.py
@@ -104,12 +104,12 @@ def build_command(
         else:
             commands_builder = CommandsBuilder(externalized_commands)
 
-    if not for_pulsar:
-        # Galaxy writes I/O files to outputs, Pulsar instruments own I/O redirection
-        io_directory = "../outputs"
-        commands_builder.capture_stdout_stderr(
-            f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
-        )
+    # Galaxy writes I/O files to outputs, Pulsar uses metadata. metadata seems like
+    # it should be preferred - at least if the directory exists.
+    io_directory = "../metadata" if for_pulsar else "../outputs"
+    commands_builder.capture_stdout_stderr(
+        f"{io_directory}/tool_stdout", f"{io_directory}/tool_stderr", stream_stdout_stderr=stream_stdout_stderr
+    )
 
     # Don't need to create a separate tool working directory for Pulsar
     # jobs - that is handled by Pulsar.
diff --git a/test/integration/test_pulsar_embedded.py b/test/integration/test_pulsar_embedded.py
index 0ea983a8a7b..f5af46a75ff 100644
--- a/test/integration/test_pulsar_embedded.py
+++ b/test/integration/test_pulsar_embedded.py
@@ -36,5 +36,6 @@ test_tools = integration_util.integration_tool_runner(
         "tool_provided_metadata_9",
         "simple_constructs_y",
         "composite_output",
+        "detect_errors",
     ]
 )