Method and apparatus for the computer-implemented processing of electronic payment instructions, wherein in a first step total instruction data contained in a payment instruction are analysed in an instruction input processor and separated into payment instruction data which are needed for processing the payment instruction and accounting data which are not needed for processing the payment instruction, the payment instruction data being converted into a uniform metaformat for processing in a subsequent payment processing apparatus (payment engine) and the accounting data being stored temporarily in a data bank together with linkage instructions, in a second step the payment instruction data converted into the metaformat are processed in the subsequent payment processing device, while, for each payee, there is automatically a routing identification and a clearing identification and, depending on the clearing identification, internal preparation of the payment instruction entry, and in a third step the automatically generated data relating to an outgoing payment instruction are converted in an instruction output processor into a target data format and are supplemented by the data which have been temporarily stored in the data bank.