How to Apply a Customer Payment to an Open Invoice in QuickBooks Online

You received a customer check payment and it is sitting on your desk and now you want to apply this payment to a specific open invoice.

  1. Go to Sales>Customers
  2. Find the customer in the list and click to open the customer’s transactions list.
  3. Scroll thru and find the invoice that you want to apply payment against and click on “Receive payment” on the right side. (Note: Some other versions of QuickBooks Online may instead state “Mark as Paid” instead of “Receive Payment”).
  4. Within the Receive Payment screen:
    1. Choose your payment date (Note: it is best to always choose a date that is AFTER the invoice date).
    2. Choose a payment method and reference number, such as the check payment number.
      1. Note: Be careful if you choose credit card, ach, check or some other payment method that may automatically trigger an electronic payment service if you subscribe to this thru QuickBooks Online.
    3. Choose your “Deposit to” account:
      1. I typically like to choose “Undeposited Funds” unless I know for sure that it is ONLY that one payment that will get deposited into the bank account very soon and by itself.
    4. Amount Received:
      1. If the settings are correct, QuickBooks will automatically complete this step for you and apply to the open invoice. However you may have to manually alter this if the customer is paying something different than what was owed on this invoice.
    5. Click Save and Close.
  5. You will now notice that open invoice is in Paid status and you will also see your payment in the list of transactions.
  6. You can verify things were done correctly by either opening your bank account register in QuickBooks Online or click on “New” (left side) and then “Bank deposit” (underneath “Other”) if your customer payment went to that Undeposited Funds account if you chose this option earlier within the Receive Payment screen.
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