QB Issue Resolution:

You can use the Receive Payment option to record the second payment. Then, make sure to select Check for the payment method. Once you save the transaction, the system will automatically set it as a credit.

 

Here are the steps:

  1. Click the Plus icon located in the upper right-hand corner.
  2. Under Customers, select Receive Payment.
  3. Choose the customer’s name from the Customer drop-down list.
  4. Select the Payment Date, and choose Check from the Payment Method drop-down list.
  5. Enter the amount in the Amount received box.
  6. Click Save and Close.
  7. You will get a prompt to save this payment as a credit, click Save as credit.

When you go to the customer’s profile, you will see an Unapplied payment. This credit can be used for future invoices.

 

You can also check this article on how to apply the credit: Apply a credit from an overpayment.

 

If you have other questions or concerns about customer transactions in QuickBooks Online, please let us know. Have a great day!

Resolution for Issue 'A customer payed me twice, once with cash and then again with a check, for the same invoice. The customer wants me to use that check for a future invoice.' available: Yes (Solved).
Source: Intuit Community forum.

A customer payed me twice, once with cash and then again with a check, for the same invoice. The customer wants me to use that check for a future invoice.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Customer Transactions
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Error Recovery for Customer Transactions [Canada]
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