diff -u b/src/Form/AdminForm.php b/src/Form/AdminForm.php
--- b/src/Form/AdminForm.php
+++ b/src/Form/AdminForm.php
@@ -22,7 +22,7 @@
 class AdminForm extends ConfigFormBase {
 
   /**
-   * @var MailsystemManager
+   * @var \Drupal\Core\Mail\MailManagerInterface
    */
   protected $mailManager;
 
@@ -41,6 +41,12 @@
    *
    * @param \Drupal\Core\Config\ConfigFactoryInterface $config_factory
    *   The factory for configuration objects.
+   * @param \Drupal\Core\Mail\MailManagerInterface $mail_manager
+   *   The mail manager.
+   * @param \Drupal\Core\Extension\ModuleHandlerInterface $module_handler
+   *   The module handler.
+   * @param \Drupal\Core\Extension\ThemeHandlerInterface $theme_handler
+   *   The theme handler.
    */
   public function __construct(ConfigFactoryInterface $config_factory, MailManagerInterface $mail_manager, ModuleHandlerInterface $module_handler, ThemeHandlerInterface $theme_handler) {
     parent::__construct($config_factory);
@@ -275,6 +281,10 @@
       $config->set('theme', $form_state->getValue(['mailsystem', 'default_theme']));
     }
 
+    // Flags to ensure if checking for each custom modules need to be updated.
+    $module_formatter = '';
+    $module_sender = '';
+
     // Create a new module configuration or update an existing one if a module
     // is selected.
     if ($form_state->hasValue(['custom', 'custom_module']) && ($form_state->getValue(['custom', 'custom_module']) != 'none')) {
@@ -291,11 +301,16 @@
       // The configuration entries can be:
       // modules.module.key.type -> Plugin for a special mail and send/format function
       // modules.module.type     -> Global plugin for the send/format function
-      $config_key = MailsystemManager::MAILSYSTEM_MODULES_CONFIG . '.' . $module;
-      $config_key .= !empty($key) ? '.' . $key : '.none';
+      $module_key = $module;
+      $module_key .= !empty($key) ? '.' . $key : '.none';
+      $config_key = MailsystemManager::MAILSYSTEM_MODULES_CONFIG . '.' . $module_key;
 
       if (!empty($config->get($config_key))) {
         // If the adding custom module already exists, then update it.
+        //if ($form_state->getValue(['custom', 'modules'])[$module_key]['formatter'] != $formatter) {
+        $module_formatter = ($config->get($config_key)['formatter'] != $formatter) ? $formatter : 'none';
+        $module_sender = ($config->get($config_key)['sender'] != $sender) ? $sender : 'none';
+
         $settings = [
           'formatter' => $formatter,
           'sender' => $sender,
@@ -305,12 +320,8 @@
       }
       else {
         // Create the new custom module configuration.
-        if ($formatter != 'none') {
-          $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $formatter);
-        }
-        if ($sender != 'none') {
-          $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $sender);
-        }
+        $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $formatter);
+        $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $sender);
       }
     }
 
@@ -318,13 +329,13 @@
     if ($form_state->hasValue(['custom', 'modules']) && is_array($form_state->getValue(['custom', 'modules']))) {
       foreach ($form_state->getValue(['custom', 'modules'], []) as $module_key => $settings) {
         $mailsystem_settings = MailsystemManager::MAILSYSTEM_MODULES_CONFIG . '.' . $module_key;
-        $formatter = (!empty($settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING])) ? $settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING] : 'none';
-        $sender = (!empty($settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING])) ? $settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING] : 'none';
+        $formatter = (($module_formatter == '') && !empty($settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING])) ? $settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING] : 'none';
+        $sender = (($module_sender == '') && !empty($settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING])) ? $settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING] : 'none';
         if (!empty($settings['remove'])) {
           // If some checkboxs are checked, remove these rows.
           $config->clear($mailsystem_settings);
         }
-        elseif (($formatter != 'none') || $sender != 'none') {
+        elseif (($formatter != 'none') || ($sender != 'none')) {
           // Update formatter and/or sender.
           $values = [
             'formatter' => $formatter,
@@ -353,6 +364,7 @@
    *   The new custom formatter/sending plugin value to be set.
    */
   protected function updateCustomModule($config, $mailsystem_settings, $values = array()) {
+    /** @var \Drupal\Core\Form\ConfigFormBase $config */
     if (($values['formatter'] != 'none') && ($values['formatter'] != $config->get($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING))) {
       $config->set($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $values['formatter']);
     }