diff -u b/src/Form/AdminForm.php b/src/Form/AdminForm.php
--- b/src/Form/AdminForm.php
+++ b/src/Form/AdminForm.php
@@ -275,7 +275,8 @@
       $config->set('theme', $form_state->getValue(['mailsystem', 'default_theme']));
     }
 
-    // Create a new module configuration if a module is selected.
+    // 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')) {
       $module = $form_state->getValue(['custom', 'custom_module']);
       $key = $form_state->getValue(['custom', 'custom_module_key']);
@@ -293,29 +294,43 @@
       $config_key = MailsystemManager::MAILSYSTEM_MODULES_CONFIG . '.' . $module;
       $config_key .= !empty($key) ? '.' . $key : '.none';
 
-      if ($formatter != 'none') {
-        $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $formatter);
+      if (!empty($config->get($config_key))) {
+        // If the adding custom module already exists, then update it.
+        $settings = [
+          'formatter' => $formatter,
+          'sender' => $sender,
+        ];
+        $this->updateCustomModule($config, $config_key, $settings);
+        $config->save();
       }
-      if ($sender != 'none') {
-        $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $sender);
+      else {
+        // Create the new custom module configuration.
+        if ($formatter != 'none') {
+          $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $formatter);
+        }
+        if ($sender != 'none') {
+          $config->set($config_key . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $sender);
+        }
       }
     }
 
+    // Update or remove the custom modules.
     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])) ? $settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING] : 'none';
         if (!empty($settings['remove'])) {
           // If some checkboxs are checked, remove these rows.
           $config->clear($mailsystem_settings);
         }
-        else {
+        elseif (($formatter != 'none') || $sender != 'none') {
           // Update formatter and/or sender.
-          if (!empty($settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING])) {
-            $config->set($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $settings[MailsystemManager::MAILSYSTEM_TYPE_FORMATTING]);
-          }
-          if (!empty($settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING])) {
-            $config->set($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $settings[MailsystemManager::MAILSYSTEM_TYPE_SENDING]);
-          }
+          $values = [
+            'formatter' => $formatter,
+            'sender' => $sender,
+          ];
+          $this->updateCustomModule($config, $mailsystem_settings, $values);
         }
       }
     }
@@ -326,6 +341,27 @@
   }
 
   /**
+   * Update the custom formatter/sending plugin value.
+   *
+   * @param string $config
+   *   The mailsystem.settings configuration object.
+   *
+   * @param string $mailsystem_settings
+   *   The custom module configuration entry to which we update the plugin.
+   *
+   * @param array $values
+   *   The new custom formatter/sending plugin value to be set.
+   */
+  protected function updateCustomModule($config, $mailsystem_settings, $values = array()) {
+    if (($values['formatter'] != 'none') && ($values['formatter'] != $config->get($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING))) {
+      $config->set($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_FORMATTING, $values['formatter']);
+    }
+    if ($values['sender'] != 'none' && ($values['sender'] != $config->get($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING))) {
+      $config->set($mailsystem_settings . '.' . MailsystemManager::MAILSYSTEM_TYPE_SENDING, $values['sender']);
+    }
+  }
+
+  /**
    * Returns a list with all formatter plugins.
    *
    * The plugin even must implement \Drupal\Core\Mail\MailInterface or the