Commerce Order email with an "Unknown" payment method (Drupal 7)
I now found the solution, I need to add the payment method to the order object, so the token system can pick it up and use in the order email.

Before save the order, we need to add the payment method.

$order-&gt;data['payment_method'] = 'bank_transfer|commerce_payment_bank_transfer';
commerce_order_save($order);


It can be placed before the transaction section.