In the Invoices menu, select Settings -> General tab. Then go to the General Settings section.
Enter payment methods that you want to uses when issuing invoices. We added some defaults, you can edit them anyway 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 WooCommerce Payment methods settings.