A credit against your supplier may arise from an over payment by your business, or when returning parts. Commonly this credit will be used to offset future payments to that supplier.
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In the Accounts Payable tab, click Make Payment, then Pay Your Creditors.
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Select your Supplier, and click Payment.
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Select your Bank Account from which you will be paying.
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Choose your payment method, either EFT or EFT Batch.
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Select the Line Items (You will see that the payment total will be all selected invoice minus the credit amount)
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Enter a Reference, Narration, and click Post.
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