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Using AccountRight Online, can a customer deposit that has been applied to an invoice be reversed?
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A customer deposit*, is not able to be reversed once that order has been converted into an invoice. In saying that, if you did need to reverse out that payment the best way is to reverse the invoice. This creates a credit note which can then be refunded to cancel out what has occurred. You can then create a new sale and payment if required. Help Article: Customer deposits goes through that process in more detail.
*A customer deposit is a payment made against an order and that order has since been converted into an invoice.