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 e8b77f14d85..d8de2ef7bb2 100644
--- a/cylc/flow/task_job_mgr.py
+++ b/cylc/flow/task_job_mgr.py
@@ -537,6 +537,12 @@ 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(
@@ -555,8 +561,11 @@ 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,
diff --git a/tests/functional/reload/28-preparing.t b/tests/functional/reload/28-preparing.t
new file mode 100644
index 00000000000..08f4ba911ac
--- /dev/null
+++ b/tests/functional/reload/28-preparing.t
@@ -0,0 +1,43 @@
+#!/usr/bin/env bash
+# THIS FILE IS PART OF THE CYLC WORKFLOW ENGINE.
+# Copyright (C) NIWA & British Crown (Met Office) & Contributors.
+# 
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#-------------------------------------------------------------------------------
+
+# Test for duplicate job submissions when preparing tasks get flushed
+# prior to reload - see https://github.com/cylc/cylc-flow/pull/6345
+
+. "$(dirname "$0")/test_header"
+set_test_number 4
+
+# Strap the process pool size down to 1, so that the first task is stuck
+# in the preparing state until the startup event handler finishes.
+
+create_test_global_config "" "
+[scheduler]
+    process pool size = 1
+"
+
+# install and play the workflow, then reload it and wait for it to finish.
+install_workflow "${TEST_NAME_BASE}" "${TEST_NAME_BASE}"
+run_ok "${TEST_NAME_BASE}-vip" cylc validate "${WORKFLOW_NAME}"
+run_ok "${TEST_NAME_BASE}-reload" cylc play "${WORKFLOW_NAME}"
+run_ok "${TEST_NAME_BASE}-reload" cylc reload "${WORKFLOW_NAME}"
+poll_grep_workflow_log -F 'INFO - DONE'
+
+# check that task `foo` was only submitted once.
+count_ok "1/foo.*submitted to" "${WORKFLOW_RUN_DIR}/log/scheduler/log" 1
+
+purge
diff --git a/tests/functional/reload/28-preparing/flow.cylc b/tests/functional/reload/28-preparing/flow.cylc
new file mode 100644
index 00000000000..27a9f1013e9
--- /dev/null
+++ b/tests/functional/reload/28-preparing/flow.cylc
@@ -0,0 +1,8 @@
+[scheduler]
+   [[events]]
+       startup handlers = "sleep 10; echo"
+[scheduling]
+    [[graph]]
+        R1 = "foo => bar"
+[runtime]
+    [[foo, bar]]