diff --git a/CIME/XML/env_batch.py b/CIME/XML/env_batch.py
index f12db7e2f0f..93545a146a0 100644
--- a/CIME/XML/env_batch.py
+++ b/CIME/XML/env_batch.py
@@ -607,7 +607,6 @@ def _process_args(self, case, submit_arg_nodes, job, resolve=True):
                 flag, name = self._get_argument(case, arg)
             except ValueError:
                 continue
-
             if self._batchtype == "cobalt" and job == "case.st_archive":
                 if flag == "-n":
                     name = "task_count"
@@ -964,7 +963,17 @@ def _submit_single_job(
 
             return
 
-        submitargs = case.get_value("BATCH_COMMAND_FLAGS", subgroup=job)
+        submitargs = case.get_value("BATCH_COMMAND_FLAGS", subgroup=job, resolved=False)
+
+        project = case.get_value("PROJECT", subgroup=job)
+
+        if not project:
+            # If there is no project then we need to remove the project flag
+            # slurm defines --account only on machines that require it, so this strip isn't required
+            if batch_system == "pbs" or batch_system == "cobalt":
+                submitargs = submitargs.replace("-A", "")
+            elif batch_system == "lsf":
+                submitargs = submitargs.replace("-P", "")
 
         if dep_jobs is not None and len(dep_jobs) > 0:
             logger.debug("dependencies: {}".format(dep_jobs))