diff --git a/lib/behat/classes/util.php b/lib/behat/classes/util.php
index 1988e015593..5338be1c7f6 100644
--- a/lib/behat/classes/util.php
+++ b/lib/behat/classes/util.php
@@ -345,6 +345,23 @@ class behat_util extends testing_util {
         return behat_command::get_parent_behat_dir() . '/test_environment_enabled.txt';
     }
 
+    /**
+     * Removes config settings that were added to the main $CFG config within the Behat CLI
+     * run.
+     *
+     * Database storage is already handled by reset_database and existing config values will
+     * be reset automatically by initialise_cfg(), so we only need to remove added ones.
+     */
+    public static function remove_added_config() {
+        global $CFG;
+        if (!empty($CFG->behat_cli_added_config)) {
+            foreach ($CFG->behat_cli_added_config as $key => $value) {
+                unset($CFG->{$key});
+            }
+            unset($CFG->behat_cli_added_config);
+        }
+    }
+
     /**
      * Reset contents of all database tables to initial values, reset caches, etc.
      */
@@ -375,6 +392,7 @@ class behat_util extends testing_util {
 
         // Initialise $CFG with default values. This is needed for behat cli process, so we don't have modified
         // $CFG values from the old run. @see set_config.
+        self::remove_added_config();
         initialise_cfg();
     }
 
diff --git a/lib/moodlelib.php b/lib/moodlelib.php
index dc8b0b0d547..c8341c5865b 100644
--- a/lib/moodlelib.php
+++ b/lib/moodlelib.php
@@ -1405,6 +1405,14 @@ function set_config($name, $value, $plugin=null) {
                 $config->value = $value;
                 $DB->insert_record('config', $config, false);
             }
+            // When setting config during a Behat test (in the CLI script, not in the web browser
+            // requests), remember which ones are set so that we can clear them later.
+            if (defined('BEHAT_TEST')) {
+                if (!property_exists($CFG, 'behat_cli_added_config')) {
+                    $CFG->behat_cli_added_config = [];
+                }
+                $CFG->behat_cli_added_config[$name] = true;
+            }
         }
         if ($name === 'siteidentifier') {
             cache_helper::update_site_identifier($value);