diff --git a/lib/galaxy/config/schemas/config_schema.yml b/lib/galaxy/config/schemas/config_schema.yml
index f2d398bcaba5..823780a856f2 100644
--- a/lib/galaxy/config/schemas/config_schema.yml
+++ b/lib/galaxy/config/schemas/config_schema.yml
@@ -1886,9 +1886,17 @@ mapping:
         required: False
         desc: |
           The upload store is a temporary directory in which files uploaded by the
-          tus middleware or server will be placed.
+          tus middleware or server for user uploads will be placed.
           Defaults to new_file_path if not set.
 
+      tus_upload_store_job_files:
+        type: str
+        required: False
+        desc: |
+          The upload store is a temporary directory in which files uploaded by the
+          tus middleware or server for remote job files (Pulsar) will be placed.
+          Defaults to tus_upload_store if not set.
+
       chunk_upload_size:
         type: int
         default: 10485760
diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py
index ab22ba72f05c..ae5ac6fe5fe7 100644
--- a/lib/galaxy/webapps/galaxy/api/job_files.py
+++ b/lib/galaxy/webapps/galaxy/api/job_files.py
@@ -103,7 +103,11 @@ def create(self, trans, job_id, payload, **kwargs):
         elif "session_id" in payload:
             # code stolen from basic.py
             session_id = payload["session_id"]
-            upload_store = trans.app.config.tus_upload_store or trans.app.config.new_file_path
+            upload_store = (
+                trans.app.config.tus_upload_store_job_files
+                or trans.app.config.tus_upload_store
+                or trans.app.config.new_file_path
+            )
             if re.match(r"^[\w-]+$", session_id) is None:
                 raise ValueError("Invalid session id format.")
             local_filename = os.path.abspath(os.path.join(upload_store, session_id))
diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py
index 3900e6f58d6a..48771bf2a73d 100644
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -1102,7 +1102,9 @@ def wrap_in_middleware(app, global_conf, application_stack, **local_conf):
         TusMiddleware,
         kwargs={
             "upload_path": urljoin(f"{application_stack.config.galaxy_url_prefix}/", "api/job_files/resumable_upload"),
-            "tmp_dir": application_stack.config.tus_upload_store or application_stack.config.new_file_path,
+            "tmp_dir": application_stack.config.tus_upload_store_job_files
+            or application_stack.config.tus_upload_store
+            or application_stack.config.new_file_path,
             "max_size": application_stack.config.maximum_upload_file_size,
         },
     )