Customer's check payment includes reversal of previous invoice payment

Thank you for taking the time to post in the Community today, LuckyDogAR. 

We'll guide you through reflecting your customer's payment in QuickBooks. However, would you mind adding more information about the scenario so we can provide the appropriate steps? Why did the customer reverse their payment? Did they return the item/s on their previous invoices, causing to reverse the payment?

Thanks in advance.

No clue.  They will probably come back and pay that invoice on a subsequent payment.  They are not disputing the invoice.  We are all in construction and it is probably a timing for projects thing.  But I need to do something with that credit.  It doesn't seem that it's a credit memo type of thing.

You're nearly there, LuckyDogAR.

Allow me to share some information on how to handle customer invoices and payments in QuickBooks Online.

We simply need to ensure that the check payment is only linked to the invoices that need to be paid and not to the previous invoice. To do this, we need to void the customer payment to unlink the previous one and recreate it again. 

But before you do, make sure the auto-apply credits setting is turned off. This way, your previous invoice will stay open after you recreate the payment. Use this as a reference to turn off the auto-apply credit feature: Create and apply credit memos or delayed credits in QuickBooks Online.

To void a payment:

1. Go to Sales, then Customers.
2. Select the customer profile.
3. Locate and open the payment. Take note of the date and amount.
4. At the bottom part, click More, and then hit Void.
5. Tap Yes to confirm.

Once done, recreate the check payment using Receive Payment.

Here's how:

1. Click on + New.
2. Select Receive payment.
3. From the Customer dropdown, pick the name of the customer.
4. From the Payment method dropdown, select check as the payment method.
5. Enter the same date and amount of the payment we voided earlier.
6. In Outstanding Transactions, choose the invoices you need to pay and exclude the previous invoice.
7. Fill in all necessary information, then click Save and close.

After that, you can check out this article to learn how to handle customer credit: Handle a customer credit or overpayment in QuickBooks Online.

If you need additional resources to manage your customer transactions, you can visit our page: Invoices and payments.

Let me know if you need further assistance or have other concerns about invoices and payments. I'll be here to help. Take care!

I think that method is going to cause problems given the payment has been reconciled.

Thanks for getting back here in the thread, @LuckyDogAR. Let's get you out of this situation to have everything in place inside QuickBooks Online (QBO).

You can write a check to have your customer's balance on that invoice available again. Doing this will also help you deal with the amount you entered inside your company file. Please be aware that you'll have to ensure the date inside that transaction is accurate. This way, we can avoid encountering issues in the future. I'll input the steps below to get you started. Here's how:

1. Inside your company file, click the +New and then select Check.
2. Choose the Payee from the dropdown ▼.
3. From the Bank account dropdown ▼, select the account the check withdraws money from.
4. Complete the check fields you need.
5. Select the Print check option if you want to open the check queue to print now. Or select the Print later checkbox if you want to print the check later.
6. Select Save and close to close the check window. Or Save and new if you need to create another check.

A reminder, if you choose a save option, this adds the check to your bank register, but only sends it to the print queue if you select Print later.

For more information, please see this article: Create and record checks in QuickBooks Online.

Now, before reconciling the account, you'll want to reach out to your accountant. This way, they can check if there's another way to handle this without affecting your past and future reconciliation.

To add up, I've got you this handy article to help you fix issues with reconciliations: Fix issues at the end of a reconciliation in QuickBooks Online.

@LuckyDogAR, I'm determined to help you sort this out. Feel free to leave comment below if you need further assistance with this. Stay safe!