diff --git a/mysql-test/r/plugin_vars.result b/mysql-test/r/plugin_vars.result
index 0e382427b1d..3fadd5e74fd 100644
--- a/mysql-test/r/plugin_vars.result
+++ b/mysql-test/r/plugin_vars.result
@@ -30,3 +30,38 @@ disconnect con2;
 USE test;
 DROP PROCEDURE p_install;
 DROP PROCEDURE p_show_vars;
+#
+# Bug#29363867: LOST CONNECTION TO MYSQL SERVER DURING QUERY
+#
+## prepared SET with a plugin variable prevents uninstall
+install plugin query_response_time soname 'query_response_time';
+prepare s from 'set global query_response_time_range_base=16';
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+plugin_status
+ACTIVE
+uninstall plugin query_response_time;
+Warnings:
+Warning	1620	Plugin is busy and will be uninstalled on shutdown
+execute s;
+execute s;
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+plugin_status
+DELETED
+deallocate prepare s;
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+plugin_status
+## prepared SET mentioning a plugin otherwise does not prevent uninstall
+install plugin archive soname 'ha_archive';
+create table t1 (a int) engine=archive;
+insert t1 values (1),(2),(3);
+prepare s from 'set session auto_increment_increment=(select count(*) from t1)';
+flush tables;
+select plugin_status from information_schema.plugins where plugin_name='archive';
+plugin_status
+ACTIVE
+uninstall plugin archive;
+select plugin_status from information_schema.plugins where plugin_name='archive';
+plugin_status
+execute s;
+ERROR 42000: Unknown storage engine 'ARCHIVE'
+drop table t1;
diff --git a/mysql-test/t/plugin_vars.test b/mysql-test/t/plugin_vars.test
index 8ba8fe2ec0e..797dcbea727 100644
--- a/mysql-test/t/plugin_vars.test
+++ b/mysql-test/t/plugin_vars.test
@@ -1,3 +1,10 @@
+if (!$QUERY_RESPONSE_TIME_SO) {
+  skip Needs query_response_time loadable plugin;
+}
+if (!$HA_ARCHIVE_SO) {
+  skip Needs Archive loadable plugin;
+}
+
 --echo #
 --echo # MDEV-5345 - Deadlock between mysql_change_user(), SHOW VARIABLES and
 --echo #             INSTALL PLUGIN
@@ -54,3 +61,31 @@ disconnect con2;
 USE test;
 DROP PROCEDURE p_install;
 DROP PROCEDURE p_show_vars;
+
+--echo #
+--echo # Bug#29363867: LOST CONNECTION TO MYSQL SERVER DURING QUERY
+--echo #
+
+--echo ## prepared SET with a plugin variable prevents uninstall
+install plugin query_response_time soname 'query_response_time';
+prepare s from 'set global query_response_time_range_base=16';
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+uninstall plugin query_response_time;
+execute s;
+execute s;
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+deallocate prepare s;
+select plugin_status from information_schema.plugins where plugin_name='query_response_time';
+
+--echo ## prepared SET mentioning a plugin otherwise does not prevent uninstall
+install plugin archive soname 'ha_archive';
+create table t1 (a int) engine=archive;
+insert t1 values (1),(2),(3);
+prepare s from 'set session auto_increment_increment=(select count(*) from t1)';
+flush tables;
+select plugin_status from information_schema.plugins where plugin_name='archive';
+uninstall plugin archive;
+select plugin_status from information_schema.plugins where plugin_name='archive';
+--error ER_UNKNOWN_STORAGE_ENGINE
+execute s;
+drop table t1;
diff --git a/sql/sql_lex.cc b/sql/sql_lex.cc
index 57c6dfad4e5..c534ba76670 100644
--- a/sql/sql_lex.cc
+++ b/sql/sql_lex.cc
@@ -765,15 +765,15 @@ void lex_end(LEX *lex)
   DBUG_ENTER("lex_end");
   DBUG_PRINT("enter", ("lex: %p", lex));
 
-  lex_end_stage1(lex);
-  lex_end_stage2(lex);
+  lex_unlock_plugins(lex);
+  lex_end_nops(lex);
 
   DBUG_VOID_RETURN;
 }
 
-void lex_end_stage1(LEX *lex)
+void lex_unlock_plugins(LEX *lex)
 {
-  DBUG_ENTER("lex_end_stage1");
+  DBUG_ENTER("lex_unlock_plugins");
 
   /* release used plugins */
   if (lex->plugins.elements) /* No function call and no mutex if no plugins. */
@@ -782,33 +782,23 @@ void lex_end_stage1(LEX *lex)
                        lex->plugins.elements);
   }
   reset_dynamic(&lex->plugins);
-
-  if (lex->context_analysis_only & CONTEXT_ANALYSIS_ONLY_PREPARE)
-  {
-    /*
-      Don't delete lex->sphead, it'll be needed for EXECUTE.
-      Note that of all statements that populate lex->sphead
-      only SQLCOM_COMPOUND can be PREPAREd
-    */
-    DBUG_ASSERT(lex->sphead == 0 || lex->sql_command == SQLCOM_COMPOUND);
-  }
-  else
-  {
-    sp_head::destroy(lex->sphead);
-    lex->sphead= NULL;
-  }
-
   DBUG_VOID_RETURN;
 }
 
 /*
+  Don't delete lex->sphead, it'll be needed for EXECUTE.
+  Note that of all statements that populate lex->sphead
+  only SQLCOM_COMPOUND can be PREPAREd
+
   MASTER INFO parameters (or state) is normally cleared towards the end
   of a statement. But in case of PS, the state needs to be preserved during
   its lifetime and should only be cleared on PS close or deallocation.
 */
-void lex_end_stage2(LEX *lex)
+void lex_end_nops(LEX *lex)
 {
-  DBUG_ENTER("lex_end_stage2");
+  DBUG_ENTER("lex_end_nops");
+  sp_head::destroy(lex->sphead);
+  lex->sphead= NULL;
 
   /* Reset LEX_MASTER_INFO */
   lex->mi.reset(lex->sql_command == SQLCOM_CHANGE_MASTER);
diff --git a/sql/sql_lex.h b/sql/sql_lex.h
index 0dab0f0666d..fbc2bf7f822 100644
--- a/sql/sql_lex.h
+++ b/sql/sql_lex.h
@@ -3412,8 +3412,8 @@ extern void lex_init(void);
 extern void lex_free(void);
 extern void lex_start(THD *thd);
 extern void lex_end(LEX *lex);
-extern void lex_end_stage1(LEX *lex);
-extern void lex_end_stage2(LEX *lex);
+extern void lex_end_nops(LEX *lex);
+extern void lex_unlock_plugins(LEX *lex);
 void end_lex_with_single_table(THD *thd, TABLE *table, LEX *old_lex);
 int init_lex_with_single_table(THD *thd, TABLE *table, LEX *lex);
 extern int MYSQLlex(union YYSTYPE *yylval, THD *thd);
diff --git a/sql/sql_prepare.cc b/sql/sql_prepare.cc
index fa335465f02..56a38757f28 100644
--- a/sql/sql_prepare.cc
+++ b/sql/sql_prepare.cc
@@ -4307,8 +4307,10 @@ bool Prepared_statement::prepare(const char *packet, uint packet_len)
     thd->release_transactional_locks();
   }
 
-  /* Preserve CHANGE MASTER attributes */
-  lex_end_stage1(lex);
+  /* Preserve locked plugins for SET */
+  if (lex->sql_command != SQLCOM_SET_OPTION)
+    lex_unlock_plugins(lex);
+
   cleanup_stmt();
   thd->restore_backup_statement(this, &stmt_backup);
   thd->stmt_arena= old_stmt_arena;
@@ -5189,7 +5191,7 @@ void Prepared_statement::deallocate_immediate()
   status_var_increment(thd->status_var.com_stmt_close);
 
   /* It should now be safe to reset CHANGE MASTER parameters */
-  lex_end_stage2(lex);
+  lex_end(lex);
 }