Payment Settings
In the Invoices menu, select Settings -> General tab. Then go to the General Settings section.
Enter payment methods that you want to use when issuing invoices. We added some defaults, you can edit them any way you want, add new or delete them. Enter one payment method per line. The above settings will be available when issuing or editing invoices manually.
WooCommerce payment methods for invoices
The plugin, when issuing invoices for WooCommerce orders, uses the payment method of the order. You may set WooCommerce payment methods settings here:
Read why payment methods may not work and how to set different payment methods for shipping.