diff --git a/mysql-test/main/bootstrap_innodb.result b/mysql-test/main/bootstrap_innodb.result
index 2807a9776a55f..7a4d88d1a920e 100644
--- a/mysql-test/main/bootstrap_innodb.result
+++ b/mysql-test/main/bootstrap_innodb.result
@@ -1,4 +1,7 @@
 create table t1(a int) engine=innodb;
+#
+# MDEV-39541 mem_pressure::~mem_pressure() causes a crash on bootstrap
+#
 # restart
 select * from t1;
 a
@@ -6,3 +9,4 @@ a
 2
 5
 drop table t1;
+# End of 10.11 tests
diff --git a/mysql-test/main/bootstrap_innodb.test b/mysql-test/main/bootstrap_innodb.test
index eb3d09c0e74ed..6606c5ecba287 100644
--- a/mysql-test/main/bootstrap_innodb.test
+++ b/mysql-test/main/bootstrap_innodb.test
@@ -22,6 +22,18 @@ EOF
 exec $MYSQLD_BOOTSTRAP_CMD --datadir=$datadir --tmpdir=$MYSQL_TMP_DIR --innodb < $MYSQLTEST_VARDIR/tmp/bootstrap_test.sql >> $MYSQLTEST_VARDIR/tmp/bootstrap.log 2>&1;
 remove_file $MYSQLTEST_VARDIR/tmp/bootstrap_test.sql;
 
+--echo #
+--echo # MDEV-39541 mem_pressure::~mem_pressure() causes a crash on bootstrap
+--echo #
+
+write_file $MYSQLTEST_VARDIR/tmp/bootstrap_test.sql;
+SHUTDOWN;
+EOF
+exec $MYSQLD_BOOTSTRAP_CMD --datadir=$datadir --tmpdir=$MYSQL_TMP_DIR --innodb < $MYSQLTEST_VARDIR/tmp/bootstrap_test.sql >> $MYSQLTEST_VARDIR/tmp/bootstrap.log 2>&1;
+remove_file $MYSQLTEST_VARDIR/tmp/bootstrap_test.sql;
+
 source include/start_mysqld.inc;
 select * from t1;
 drop table t1;
+
+--echo # End of 10.11 tests
diff --git a/sql/mysqld.cc b/sql/mysqld.cc
index 3b49c53c52b26..71b826927d1c3 100644
--- a/sql/mysqld.cc
+++ b/sql/mysqld.cc
@@ -1667,7 +1667,8 @@ static void break_connect_loop()
   abort_loop= 1;
 
 #if defined(_WIN32)
-  mysqld_win_initiate_shutdown();
+  if (!opt_bootstrap)
+    mysqld_win_initiate_shutdown();
 #else
   mysql_mutex_lock(&LOCK_start_thread);
   if (termination_event_fd >= 0)
@@ -1842,12 +1843,6 @@ static void close_connections(void)
   }
   /* End of kill phase 2 */
 
-  /*
-    The signal thread can use server resources, e.g. when processing SIGHUP,
-    and it must end gracefully before clean_up()
-  */
-  wait_for_signal_thread_to_end();
-
   DBUG_PRINT("quit",("close_connections thread"));
   DBUG_VOID_RETURN;
 }
@@ -2079,7 +2074,6 @@ static void clean_up(bool print_message)
 
 
 #ifndef EMBEDDED_LIBRARY
-
 /**
   This is mainly needed when running with purify, but it's still nice to
   know that all child threads have died when mysqld exits.
@@ -6041,10 +6035,7 @@ int mysqld_main(int argc, char **argv)
     if (!abort_loop)
       unireg_abort(bootstrap_error);
     else
-    {
-      sleep(2);                                 // Wait for kill
-      exit(0);
-    }
+      goto termination;
   }
 
   /* Copy default global rpl_filter to global_rpl_filter */
@@ -6119,11 +6110,11 @@ int mysqld_main(int argc, char **argv)
   run_main_loop();
 
   /* Shutdown requested */
-  char *user= shutdown_user.load(std::memory_order_relaxed);
-  sql_print_information(ER_DEFAULT(ER_NORMAL_SHUTDOWN), my_progname,
+  {
+    char *user= shutdown_user.load(std::memory_order_relaxed);
+    sql_print_information(ER_DEFAULT(ER_NORMAL_SHUTDOWN), my_progname,
                         user ? user : "unknown");
-  if (user)
-    my_free(user);
+  }
 
 #ifdef WITH_WSREP
   wsrep_shutdown();
@@ -6132,6 +6123,19 @@ int mysqld_main(int argc, char **argv)
 #endif
 
   close_connections();
+
+termination:
+  {
+    char *user= shutdown_user.load(std::memory_order_relaxed);
+    if (user)
+      my_free(user);
+  }
+  /*
+    The signal thread can use server resources, e.g. when processing SIGHUP,
+    and it must end gracefully before clean_up()
+  */
+  wait_for_signal_thread_to_end();
+
   ha_pre_shutdown();
   clean_up(1);
   sd_notify(0, "STATUS=MariaDB server is down");
diff --git a/storage/innobase/handler/ha_innodb.cc b/storage/innobase/handler/ha_innodb.cc
index 2665fa0012f35..37c1bcefde468 100644
--- a/storage/innobase/handler/ha_innodb.cc
+++ b/storage/innobase/handler/ha_innodb.cc
@@ -4273,6 +4273,8 @@ innobase_end(handlerton*, ha_panic_function)
 		innodb_shutdown();
 		mysql_mutex_destroy(&log_requests.mutex);
 	}
+	else
+		buf_mem_pressure_shutdown();
 
 	DBUG_RETURN(0);
 }
diff --git a/storage/innobase/include/srv0start.h b/storage/innobase/include/srv0start.h
index e562458722c75..27d953311d911 100644
--- a/storage/innobase/include/srv0start.h
+++ b/storage/innobase/include/srv0start.h
@@ -52,6 +52,12 @@ void innodb_preshutdown();
 /** Shut down InnoDB. */
 void innodb_shutdown();
 
+/** Stop mem presure thread and free file descriptors */
+#ifdef __linux__
+void buf_mem_pressure_shutdown() noexcept;
+#else
+inline void buf_mem_pressure_shutdown() noexcept {}
+#endif
 /*************************************************************//**
 Copy the file path component of the physical file to parameter. It will
 copy up to and including the terminating path separator.
diff --git a/storage/innobase/log/log0log.cc b/storage/innobase/log/log0log.cc
index fe951c49406f3..763f95295583f 100644
--- a/storage/innobase/log/log0log.cc
+++ b/storage/innobase/log/log0log.cc
@@ -1351,12 +1351,6 @@ void log_free_check() noexcept
   }
 }
 
-#ifdef __linux__
-extern void buf_mem_pressure_shutdown() noexcept;
-#else
-inline void buf_mem_pressure_shutdown() noexcept {}
-#endif
-
 /** Make a checkpoint at the latest lsn on shutdown.
 @return the shutdown LSN */
 ATTRIBUTE_COLD lsn_t logs_empty_and_mark_files_at_shutdown() noexcept