diff --git a/changes.d/6345.fix.md b/changes.d/6345.fix.md
new file mode 100644
index 00000000000..a629eb6c8ed
--- /dev/null
+++ b/changes.d/6345.fix.md
@@ -0,0 +1 @@
+Fix duplicate job submissions of tasks in the preparing state before reload.
diff --git a/cylc/flow/task_job_mgr.py b/cylc/flow/task_job_mgr.py
index 185966ff12d..d5c98288294 100644
--- a/cylc/flow/task_job_mgr.py
+++ b/cylc/flow/task_job_mgr.py
@@ -536,6 +536,12 @@ def submit_task_jobs(self, workflow, itasks, curve_auth,
                 stdin_files = []
                 job_log_dirs = []
                 for itask in itasks_batch:
+                    if not itask.waiting_on_job_prep:
+                        # Avoid duplicate job submissions when flushing
+                        # preparing tasks before a reload. See
+                        # https://github.com/cylc/cylc-flow/pull/6345
+                        continue
+
                     if remote_mode:
                         stdin_files.append(
                             os.path.expandvars(
@@ -554,8 +560,11 @@ def submit_task_jobs(self, workflow, itasks, curve_auth,
                     # write flag so that subsequent manual retrigger will
                     # generate a new job file.
                     itask.local_job_file_path = None
-
                     itask.waiting_on_job_prep = False
+
+                if not job_log_dirs:
+                    continue
+
                 self.proc_pool.put_command(
                     SubProcContext(
                         self.JOBS_SUBMIT,