diff --git a/admin/cli/maintenance.php b/admin/cli/maintenance.php
index b267a039c31..b77cdcf537a 100644
--- a/admin/cli/maintenance.php
+++ b/admin/cli/maintenance.php
@@ -69,7 +69,7 @@ if ($options['enablelater']) {
     }
 
     $time = time() + ($options['enablelater']*60);
-    set_config('maintenance_later', $time);
+    set_config('maintenance_later', $time, null, true);
 
     echo get_string('clistatusenabledlater', 'admin', userdate($time))."\n";
     return 0;
@@ -77,23 +77,32 @@ if ($options['enablelater']) {
 } else if ($options['enable']) {
     if (file_exists("$CFG->dataroot/climaintenance.html")) {
         // The maintenance is already enabled, nothing to do.
-    } else {
-        enable_cli_maintenance_mode();
+        exit(0);
+    }
+    enable_cli_maintenance_mode();
+    set_config('maintenance_enabled', 'cli mode', null, true);
+
+    if (isset($CFG->maintenance_later)) {
+        unset_config('maintenance_later', null, true);
     }
-    set_config('maintenance_enabled', 0);
-    unset_config('maintenance_later');
     echo get_string('sitemaintenanceoncli', 'admin')."\n";
     exit(0);
 
 } else if ($options['enableold']) {
-    set_config('maintenance_enabled', 1);
-    unset_config('maintenance_later');
+    set_config('maintenance_enabled', 1, null, true);
+    if (isset($CFG->maintenance_later)) {
+        unset_config('maintenance_later', null, true);
+    }
     echo get_string('sitemaintenanceon', 'admin')."\n";
     exit(0);
 
 } else if ($options['disable']) {
-    set_config('maintenance_enabled', 0);
-    unset_config('maintenance_later');
+    if ($CFG->maintenance_enabled !== '0') {
+        set_config('maintenance_enabled', 0, null, true);
+    }
+    if (isset($CFG->maintenance_later)) {
+        unset_config('maintenance_later', null, true);
+    }
     if (file_exists("$CFG->dataroot/climaintenance.html")) {
         unlink("$CFG->dataroot/climaintenance.html");
     }
diff --git a/public/lib/moodlelib.php b/public/lib/moodlelib.php
index c140d575667..102e4afe6ac 100644
--- a/public/lib/moodlelib.php
+++ b/public/lib/moodlelib.php
@@ -934,14 +934,23 @@ function html_is_blank($string) {
  * @param string|int|bool|null $value the value to set (without magic quotes),
  *               null to unset the value
  * @param string $plugin (optional) the plugin scope, default null
+ * @param boolean $log (optional) should this emit to the config log
  * @return bool true or exception
  */
-function set_config($name, $value, $plugin = null) {
+function set_config($name, $value, $plugin = null, bool $log = false) {
     global $CFG, $DB;
 
     // Redirect to appropriate handler when value is null.
     if ($value === null) {
-        return unset_config($name, $plugin);
+        return unset_config($name, $plugin, $log);
+    }
+
+    if ($log) {
+        $prev = get_config($plugin, $name);
+        if ($prev === false) {
+            $prev = null;
+        }
+        add_to_config_log($name, $prev, $value, $plugin);
     }
 
     // Set variables determining conditions and where to store the new config.
@@ -1099,11 +1108,20 @@ function get_config($plugin, $name = null) {
  *
  * @param string $name the key to set
  * @param string $plugin (optional) the plugin scope
+ * @param boolean $log (optional) should this emit to the config log
  * @return boolean whether the operation succeeded.
  */
-function unset_config($name, $plugin=null) {
+function unset_config($name, $plugin = null, bool $log = false) {
     global $CFG, $DB;
 
+    if ($log) {
+        $prev = get_config($plugin, $name);
+        if ($prev === false) {
+            $prev = null;
+        }
+        add_to_config_log($name, $prev, null, $plugin);
+    }
+
     if (empty($plugin)) {
         unset($CFG->$name);
         $DB->delete_records('config', array('name' => $name));
diff --git a/public/lib/setup.php b/public/lib/setup.php
index b79c7782a0e..575bd41eb03 100644
--- a/public/lib/setup.php
+++ b/public/lib/setup.php
@@ -1160,15 +1160,27 @@ if (!empty($_SERVER['HTTP_USER_AGENT']) and strpos($_SERVER['HTTP_USER_AGENT'],
 
 // Switch to CLI maintenance mode if required, we need to do it here after all the settings are initialised.
 if (isset($CFG->maintenance_later) and $CFG->maintenance_later <= time()) {
+
+    // Because maintenance_later is triggered by any potentially real non admin user
+    // who just happened to be the first to load a page after the time is due, we do
+    // this simple workaround so add_to_config_log doesn't log it as them.
+    \core\session\manager::write_close();
+    $USER->id = 0;
+
     if (!file_exists("$CFG->dataroot/climaintenance.html")) {
         require_once("$CFG->libdir/adminlib.php");
+        set_config('maintenance_enabled', 'cli mode', null, true);
         enable_cli_maintenance_mode();
     }
-    unset_config('maintenance_later');
+    if (isset($CFG->maintenance_later)) {
+        unset_config('maintenance_later', null, true);
+    }
     if (AJAX_SCRIPT) {
         die;
     } else if (!CLI_SCRIPT) {
-        redirect(new moodle_url('/'));
+        // We redirect to ourselves to reload the page to get a fresh bootstrap
+        // so that we get the maintenance page which is earlier in setup.
+        redirect(new moodle_url($ME));
     }
 }