A system and method for optimal selection of payment authorization in a complex commerce system is presented. A commerce system uses an algorithm to select an optimum payment authorization for a particular payment deposit. The algorithm allows the commerce system to support multiple types of authorizations while minimizing the number of payment transactions if possible. The algorithm also handles payment instrument priority, sufficient authorization amount availability, and a selection of a favorable set of payment authorizations for which to apply the payment deposit. Once the algorithm selects an optimum payment authorization for a particular payment deposit, the commerce system applies the payment deposit towards the optimum payment authorization in order to receive funds from an external payment provider.