How are organizations that have implemented the commercial card program of paying for purchase order invoices with card are able to close the PO in their financial systems? What are the processes after payment is made to integrate payment and PO closure?

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If AP is closing the invoice with a credit card, enter a prepaid invoice against the PO.   This closes the PO and the prepaid invoice books all the appropriate GL accounts and does not trigger a check or other method of payment.  This also leaves a good audit trail and the invoice is in history for duplicate checks.

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