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Receiving Payment Against an Invoice in QuickBooks
To record a payment received against an open invoice in QuickBooks, make sure to use the Receive Payments window. New QuickBooks users often make the mistake of recording the payment directly into the check register, which results in erroneous reports (P&L is wrong because income is counted twice - once when the invoice was created and again when the payment was received, AR reports will be incorrect) and messy books (an invoice is left open that you are no longer awaiting payment on). Therefore, if you use invoices in QuickBooks, then remember to use the Receive Payments window.
Open the Receive Payments window from the Customer menu.
In the Receive Payments window, fill out the Received From field, the Amount received, Date received, Pmt. Method and Check #. Then select the appropriate invoice to apply the payment to (QuickBooks will make a guess - change it if QuickBooks guessed wrong). Then Save.
After receiving payment, remember that it won't show up in your bank account register in QuickBooks until you deposit it (from the Banking menu, select Make Deposits).
