A system, apparatus, and method for processing payment transactions that are conducted using a mobile payment device that includes a contactless element, such as an integrated circuit chip. The invention enables one or more of the operations of activation of a payment application, transfer of transaction data, updating of account records, setting or re-setting of a payment application counter or register, or transfer or processing of a script, command, or instruction, with these functions being performed with minimal impact on a consumer. This is accomplished by introducing a pre-tap and/or two-tap operation prior to, or as part of, the transaction flow.