Abstract: A system and method of batch processing payment transactions comprises a memory unit and a processor. The processor executes a set of program modules comprising an input module, a payment batching module, and a payment transaction processor module. The input module receives information associated with at least one transaction bundle. The at least one transaction bundle comprises at least one payment transaction associated with a first payment destination account. The payment batching module assigns a second payment destination account to a payment batch among a plurality of payment batches. The payment batching module selectively assigns the at least one payment transaction to the payment batch, based on the first payment destination account being identical to the second payment destination account. The payment transaction processor module processes the at least one payment transaction in the plurality of payment batches on a batch basis.