diff --git a/mysql-test/suite/rpl/r/rpl_parallel_ftwrl.result b/mysql-test/suite/rpl/r/rpl_parallel_ftwrl.result
new file mode 100644
index 00000000000..b6c71055fe7
--- /dev/null
+++ b/mysql-test/suite/rpl/r/rpl_parallel_ftwrl.result
@@ -0,0 +1,105 @@
+include/master-slave.inc
+[connection master]
+connection slave;
+include/stop_slave.inc
+SET @old_parallel_threads= @@GLOBAL.slave_parallel_threads;
+SET GLOBAL slave_parallel_threads=3;
+SET @old_parallel_mode= @@GLOBAL.slave_parallel_mode;
+SET GLOBAL slave_parallel_mode=aggressive;
+SET @old_dbug= @@GLOBAL.debug_dbug;
+CHANGE MASTER TO master_use_gtid=slave_pos;
+include/start_slave.inc
+*** MDEV-31509: Lost data with FTWRL and STOP SLAVE
+connection master;
+ALTER TABLE mysql.gtid_slave_pos ENGINE=InnoDB;
+CREATE TABLE t1 (a INT PRIMARY KEY, b INT) ENGINE=InnoDB;
+CREATE TABLE t2 (a INT PRIMARY KEY, b INT) ENGINE=MyISAM;
+INSERT INTO t1 VALUES (0,0);
+INSERT INTO t2 VALUES (0,0);
+include/save_master_gtid.inc
+connection slave;
+include/sync_with_master_gtid.inc
+connection slave;
+*** Arrange for T1 to delay before entering GCO wait.
+SET GLOBAL debug_dbug="+d,gco_wait_delay_gtid_0_x_99";
+*** Arrange for T2 to wait for FTWRL to start.
+SET GLOBAL debug_dbug="+d,hold_worker_on_schedule";
+*** Arrange for T2 to delay wakeup from FTWRL pause.
+SET GLOBAL debug_dbug="+d,delay_ftwrl_wait_gtid_0_x_100";
+connection master;
+*** Event group T1
+SET SESSION gtid_seq_no=99;
+INSERT INTO t1 VALUES (1,1);
+connection slave;
+*** 1a. Wait for T1 to be queued.
+SET debug_sync="now WAIT_FOR gco_wait_paused";
+connection master;
+*** Event group T2
+SET SESSION gtid_seq_no=100;
+INSERT INTO t2 VALUES (2,2);
+connection slave;
+*** 1b. Wait for T2 to be queued.
+SET debug_sync= "now WAIT_FOR reached_pause";
+connection slave1;
+*** 2. Run FTWRL
+SET GLOBAL debug_dbug= "+d,pause_for_ftwrl_wait";
+FLUSH TABLES WITH READ LOCK;
+connection slave;
+SET debug_sync= "now WAIT_FOR pause_ftwrl_waiting";
+*** 3. Wait for T2 to be waiting for FTWRL pause
+SET debug_sync= "now SIGNAL continue_worker";
+*** 4. FTWRL completes, UNLOCK TABLES.
+SET debug_sync="now SIGNAL pause_ftwrl_cont";
+connection slave1;
+UNLOCK TABLES;
+connection slave;
+*** T2 is now ready to proceed after FTWRL pause, but did not wake up yet.
+SET debug_sync="now WAIT_FOR pause_wait_started";
+*** 5. STOP SLAVE is run.
+connection slave1;
+SET GLOBAL debug_dbug="+d,rpl_parallel_wait_for_done_trigger";
+STOP SLAVE;
+connection slave;
+SET debug_sync="now WAIT_FOR wait_for_done_waiting";
+*** 5. T2 wakes up after FTWRL pause, reaches wait_for_prior_commit().
+SET debug_sync="now SIGNAL pause_wait_continue";
+*** 6. T1 starts.
+SET debug_sync="now SIGNAL gco_wait_cont";
+connection slave1;
+connection slave;
+include/wait_for_slave_to_stop.inc
+connection master;
+SELECT * FROM t1 ORDER BY a;
+a	b
+0	0
+1	1
+SELECT * FROM t2 ORDER BY a;
+a	b
+0	0
+2	2
+include/save_master_gtid.inc
+connection slave;
+include/start_slave.inc
+include/sync_with_master_gtid.inc
+SELECT @@GLOBAL.gtid_slave_pos;
+@@GLOBAL.gtid_slave_pos
+0-1-100
+SELECT * FROM t1 ORDER BY a;
+a	b
+0	0
+1	1
+SELECT * FROM t2 ORDER BY a;
+a	b
+0	0
+2	2
+*** Clean up.
+connection slave;
+include/stop_slave.inc
+SET DEBUG_SYNC= "RESET";
+SET GLOBAL slave_parallel_threads= @old_parallel_threads;
+SET GLOBAL slave_parallel_mode= @old_parallel_mode;
+SET GLOBAL debug_dbug=@old_dbug;
+include/start_slave.inc
+connection master;
+DROP TABLE t1, t2;
+include/rpl_end.inc
diff --git a/mysql-test/suite/rpl/t/rpl_parallel_ftwrl.test b/mysql-test/suite/rpl/t/rpl_parallel_ftwrl.test
new file mode 100644
index 00000000000..308fcd0bd1f
--- /dev/null
+++ b/mysql-test/suite/rpl/t/rpl_parallel_ftwrl.test
@@ -0,0 +1,143 @@
+--source include/have_innodb.inc
+--source include/have_debug.inc
+--source include/have_debug_sync.inc
+--source include/have_binlog_format_mixed.inc
+--source include/master-slave.inc
+
+--connection slave
+--source include/stop_slave.inc
+SET @old_parallel_threads= @@GLOBAL.slave_parallel_threads;
+SET GLOBAL slave_parallel_threads=3;
+SET @old_parallel_mode= @@GLOBAL.slave_parallel_mode;
+SET GLOBAL slave_parallel_mode=aggressive;
+SET @old_dbug= @@GLOBAL.debug_dbug;
+CHANGE MASTER TO master_use_gtid=slave_pos;
+--source include/start_slave.inc
+
+--echo *** MDEV-31509: Lost data with FTWRL and STOP SLAVE
+# The bug was as follows:
+# 1. Event groups T1 and T2 are queued but not started yet.
+# 2. FLUSH TABLE WITH READ LOCKS starts, sets rpl_parallel_entry::pause_sub_id
+# 3. T2 Sees pause_sub_id, goes to wait for the pause to complete.
+# 4. FTWRL completes, UNLOCK TABLES is run.
+# 5. STOP SLAVE is run, sets rpl_parallel_entry::stop_sub_id.
+# 6. T2 wakes up after FTWRL pause, only now sets
+#    rpl_parallel_entry::largest_started_sub_id. This is the bug,
+#    largest_started_sub_id is set too late here.
+# 7. T1 starts, it sees stop_sub_id<T1, so T1 is skipped due to STOP SLAVE.
+# 8. T2 continues, its check for stop_sub_id was before STOP SLAVE. So T2 is
+#    wrongly applied, silently losing transaction T1.
+
+
+--connection master
+ALTER TABLE mysql.gtid_slave_pos ENGINE=InnoDB;
+CREATE TABLE t1 (a INT PRIMARY KEY, b INT) ENGINE=InnoDB;
+CREATE TABLE t2 (a INT PRIMARY KEY, b INT) ENGINE=MyISAM;
+INSERT INTO t1 VALUES (0,0);
+INSERT INTO t2 VALUES (0,0);
+--source include/save_master_gtid.inc
+
+--connection slave
+--source include/sync_with_master_gtid.inc
+
+--connection slave
+--echo *** Arrange for T1 to delay before entering GCO wait.
+SET GLOBAL debug_dbug="+d,gco_wait_delay_gtid_0_x_99";
+--echo *** Arrange for T2 to wait for FTWRL to start.
+SET GLOBAL debug_dbug="+d,hold_worker_on_schedule";
+--echo *** Arrange for T2 to delay wakeup from FTWRL pause.
+SET GLOBAL debug_dbug="+d,delay_ftwrl_wait_gtid_0_x_100";
+
+--connection master
+--echo *** Event group T1
+SET SESSION gtid_seq_no=99;
+INSERT INTO t1 VALUES (1,1);
+
+--connection slave
+--echo *** 1a. Wait for T1 to be queued.
+SET debug_sync="now WAIT_FOR gco_wait_paused";
+
+--connection master
+--echo *** Event group T2
+SET SESSION gtid_seq_no=100;
+INSERT INTO t2 VALUES (2,2);
+
+--connection slave
+--echo *** 1b. Wait for T2 to be queued.
+SET debug_sync= "now WAIT_FOR reached_pause";
+
+--connection slave1
+--echo *** 2. Run FTWRL
+SET GLOBAL debug_dbug= "+d,pause_for_ftwrl_wait";
+send FLUSH TABLES WITH READ LOCK;
+
+--connection slave
+SET debug_sync= "now WAIT_FOR pause_ftwrl_waiting";
+
+--echo *** 3. Wait for T2 to be waiting for FTWRL pause
+SET debug_sync= "now SIGNAL continue_worker";
+--let $wait_condition= SELECT count(*) = 1 FROM information_schema.processlist WHERE state LIKE "%Waiting due to global read lock%" and command="Slave_worker";
+--source include/wait_condition.inc
+
+--echo *** 4. FTWRL completes, UNLOCK TABLES.
+SET debug_sync="now SIGNAL pause_ftwrl_cont";
+
+--connection slave1
+reap;
+UNLOCK TABLES;
+
+--connection slave
+--echo *** T2 is now ready to proceed after FTWRL pause, but did not wake up yet.
+SET debug_sync="now WAIT_FOR pause_wait_started";
+
+--echo *** 5. STOP SLAVE is run.
+--connection slave1
+SET GLOBAL debug_dbug="+d,rpl_parallel_wait_for_done_trigger";
+send STOP SLAVE;
+
+--connection slave
+SET debug_sync="now WAIT_FOR wait_for_done_waiting";
+
+--echo *** 5. T2 wakes up after FTWRL pause, reaches wait_for_prior_commit().
+SET debug_sync="now SIGNAL pause_wait_continue";
+--let $wait_condition= SELECT count(*) = 1 FROM information_schema.processlist WHERE state LIKE "%Waiting for prior transaction to commit%" and command="Slave_worker";
+--source include/wait_condition.inc
+
+--echo *** 6. T1 starts.
+SET debug_sync="now SIGNAL gco_wait_cont";
+
+--connection slave1
+reap;
+
+--connection slave
+--source include/wait_for_slave_to_stop.inc
+
+--connection master
+SELECT * FROM t1 ORDER BY a;
+SELECT * FROM t2 ORDER BY a;
+--source include/save_master_gtid.inc
+
+--connection slave
+--source include/start_slave.inc
+--source include/sync_with_master_gtid.inc
+
+# The bug here was that T2 was errorneously replicated while T1 was
+# being skipped due to STOP SLAVE. So the @@gtid_slave_pos was at T2,
+# but we were missing the data from T1.
+SELECT @@GLOBAL.gtid_slave_pos;
+SELECT * FROM t1 ORDER BY a;
+SELECT * FROM t2 ORDER BY a;
+
+--echo *** Clean up.
+--connection slave
+--source include/stop_slave.inc
+SET DEBUG_SYNC= "RESET";
+SET GLOBAL slave_parallel_threads= @old_parallel_threads;
+SET GLOBAL slave_parallel_mode= @old_parallel_mode;
+SET GLOBAL debug_dbug=@old_dbug;
+--source include/start_slave.inc
+
+--connection master
+DROP TABLE t1, t2;
+
+--source include/rpl_end.inc
diff --git a/sql/rpl_parallel.cc b/sql/rpl_parallel.cc
index ed8858d67ba..ad9c2ac802c 100644
--- a/sql/rpl_parallel.cc
+++ b/sql/rpl_parallel.cc
@@ -369,7 +369,7 @@ register_wait_for_prior_event_group_commit(rpl_group_info *rgi,
   Do not start parallel execution of this event group until all prior groups
   have reached the commit phase that are not safe to run in parallel with.
 */
-static bool
+static void
 do_gco_wait(rpl_group_info *rgi, group_commit_orderer *gco,
             bool *did_enter_cond, PSI_stage_info *old_stage)
 {
@@ -421,8 +421,18 @@ do_gco_wait(rpl_group_info *rgi, group_commit_orderer *gco,
                       &entry->LOCK_parallel_entry);
     } while (wait_count > entry->count_committing_event_groups);
   }
+}
 
-  if (entry->force_abort && rgi->gtid_sub_id > entry->stop_sub_id)
+
+static bool
+do_stop_handling(rpl_group_info *rgi)
+{
+  bool should_stop= false;
+  rpl_parallel_entry *entry=  rgi->parallel_entry;
+
+  mysql_mutex_assert_owner(&entry->LOCK_parallel_entry);
+
+  if (unlikely(entry->force_abort) && rgi->gtid_sub_id > entry->stop_sub_id)
   {
     /*
       We are stopping (STOP SLAVE), and this event group need not be applied
@@ -430,10 +440,26 @@ do_gco_wait(rpl_group_info *rgi, group_commit_orderer *gco,
       rather than execute, the following events. Once all queued events have
       been skipped, the STOP SLAVE is complete (for this thread).
     */
-    return true;
+    should_stop= true;
   }
-  else
-    return false;
+
+  if (unlikely(entry->stop_on_error_sub_id <= rgi->wait_commit_sub_id))
+  {
+    rgi->worker_error= 1;
+    should_stop= true;
+  }
+
+  if (likely(!should_stop))
+  {
+    /*
+      Since we did not decide to stop, bump the largest_started_sub_id while
+      still holding LOCK_parallel_entry.
+    */
+    if (rgi->gtid_sub_id > entry->largest_started_sub_id)
+      entry->largest_started_sub_id= rgi->gtid_sub_id;
+  }
+
+  return should_stop;
 }
 
 
@@ -480,15 +506,25 @@ do_ftwrl_wait(rpl_group_info *rgi,
       mysql_cond_wait(&entry->COND_parallel_entry, &entry->LOCK_parallel_entry);
     } while (sub_id > entry->pause_sub_id);
 
+    DBUG_EXECUTE_IF("delay_ftwrl_wait_gtid_0_x_100", {
+        if (rgi->current_gtid.domain_id == 0 &&
+            rgi->current_gtid.seq_no == 100) {
+          /*
+            Simulate delayed wakeup from the mysql_cond_wait(). To do this, we
+            need to have the LOCK_parallel_entry mutex released during the wait.
+          */
+          mysql_mutex_unlock(&entry->LOCK_parallel_entry);
+          debug_sync_set_action(thd,
+              STRING_WITH_LEN("now SIGNAL pause_wait_started WAIT_FOR pause_wait_continue"));
+          mysql_mutex_lock(&entry->LOCK_parallel_entry);
+        }
+      });
     /*
       We do not call EXIT_COND() here, as this will be done later by our
       caller (since we set *did_enter_cond to true).
     */
   }
 
-  if (sub_id > entry->largest_started_sub_id)
-    entry->largest_started_sub_id= sub_id;
-
   DBUG_RETURN(aborted);
 }
 
@@ -646,7 +682,17 @@ rpl_pause_for_ftwrl(THD *thd)
     mysql_mutex_unlock(&rpt->LOCK_rpl_thread);
     ++e->need_sub_id_signal;
     if (e->pause_sub_id == (uint64)ULONGLONG_MAX)
+    {
       e->pause_sub_id= e->largest_started_sub_id;
+      DBUG_EXECUTE_IF("pause_for_ftwrl_wait", {
+          mysql_mutex_unlock(&e->LOCK_parallel_entry);
+          debug_sync_set_action(thd,
+                                STRING_WITH_LEN("now "
+                                                "SIGNAL pause_ftwrl_waiting "
+                                                "WAIT_FOR pause_ftwrl_cont"));
+          mysql_mutex_lock(&e->LOCK_parallel_entry);
+        });
+    }
     thd->ENTER_COND(&e->COND_parallel_entry, &e->LOCK_parallel_entry,
                     &stage_waiting_for_ftwrl_threads_to_pause, &old_stage);
     thd->set_time_for_next_stage();
@@ -1284,14 +1330,15 @@ handle_rpl_parallel_thread(void *arg)
         event_gtid_sub_id= rgi->gtid_sub_id;
         rgi->thd= thd;
 
-        mysql_mutex_lock(&entry->LOCK_parallel_entry);
-        skip_event_group= do_gco_wait(rgi, gco, &did_enter_cond, &old_stage);
+        DBUG_EXECUTE_IF("gco_wait_delay_gtid_0_x_99", {
+            if (rgi->current_gtid.domain_id == 0 && rgi->current_gtid.seq_no == 99) {
+              debug_sync_set_action(thd,
+                  STRING_WITH_LEN("now SIGNAL gco_wait_paused WAIT_FOR gco_wait_cont"));
+            } });
 
-        if (unlikely(entry->stop_on_error_sub_id <= rgi->wait_commit_sub_id))
-        {
-          skip_event_group= true;
-          rgi->worker_error= 1;
-        }
+        mysql_mutex_lock(&entry->LOCK_parallel_entry);
+        do_gco_wait(rgi, gco, &did_enter_cond, &old_stage);
+        skip_event_group= do_stop_handling(rgi);
         if (likely(!skip_event_group))
           skip_event_group= do_ftwrl_wait(rgi, &did_enter_cond, &old_stage);