diff --git a/mysql-test/main/alter_table_online.result b/mysql-test/main/alter_table_online.result
index 5015b4cb5b7..903fa86de94 100644
--- a/mysql-test/main/alter_table_online.result
+++ b/mysql-test/main/alter_table_online.result
@@ -54,3 +54,22 @@ c	c2	stamp
 5	5	0000-00-00 00:00:00
 drop table t;
 set sql_mode=default;
+#
+# MDEV-28944 XA assertions failing in binlog_rollback and binlog_commit
+#
+CREATE TABLE t (a INT) ENGINE=MyISAM;
+INSERT INTO t VALUES (1);
+connect  con1,localhost,root,,test;
+XA START 'xid';
+SELECT * FROM t;
+a
+1
+connection default;
+ALTER TABLE t NOWAIT ADD KEY (a);
+ERROR HY000: Lock wait timeout exceeded; try restarting transaction
+connection con1;
+UPDATE t SET a = 2;
+XA END 'xid';
+XA COMMIT 'xid' ONE PHASE;
+DROP TABLE t;
+disconnect con1;
diff --git a/mysql-test/main/alter_table_online.test b/mysql-test/main/alter_table_online.test
index a9e20fa05f6..92710f46cbf 100644
--- a/mysql-test/main/alter_table_online.test
+++ b/mysql-test/main/alter_table_online.test
@@ -33,3 +33,25 @@ alter table t modify c date;
 select * from t;
 drop table t;
 set sql_mode=default;
+
+--echo #
+--echo # MDEV-28944 XA assertions failing in binlog_rollback and binlog_commit
+--echo #
+CREATE TABLE t (a INT) ENGINE=MyISAM;
+INSERT INTO t VALUES (1);
+
+--connect (con1,localhost,root,,test)
+XA START 'xid';
+SELECT * FROM t;
+
+--connection default
+--error ER_LOCK_WAIT_TIMEOUT
+ALTER TABLE t NOWAIT ADD KEY (a);
+
+--connection con1
+UPDATE t SET a = 2;
+XA END 'xid';
+XA COMMIT 'xid' ONE PHASE;
+
+DROP TABLE t;
+--disconnect con1
diff --git a/sql/sql_table.cc b/sql/sql_table.cc
index 7e9663b5656..80ceebfe277 100644
--- a/sql/sql_table.cc
+++ b/sql/sql_table.cc
@@ -12011,6 +12011,8 @@ copy_data_between_tables(THD *thd, TABLE *from, TABLE *to,
       thd_progress_next_stage(thd);
       error= online_alter_read_from_binlog(thd, &rgi, binlog);
     }
+    if (error)
+      from->s->tdc->flush_unused(1); // to free the binlog
   }
   else if (online) // error was on copy stage
   {