How do I delete unapplied payments after removing Sync for Square?

Hello there, kito2020.

Thanks for posting here!

You can manually delete those payments. Let's open the payment transaction. Then, click on More and select Delete. You can also refer to this article for additional details:

• Void or delete transactions in QuickBooks Online

Post again if you need anything else. Wishing you all the best!

Hello,

The Sync for Square app brought in the sales as individual “Invoices” on the Sales tab with payments applied. I deleted all the invoices, but I am left with the payments, which are showing in Unapplied Payments. When I click on one of these payments under the “Sales” tab, it opens ALL of the payments and shows them as “Credits.” There is no option to delete or void any of these. It appears it wants me to apply these payments/credits to an invoice but they are all duplicates and need to go completely away.

Does that make sense? 

Hello,

Sync for Square imported the sales as individual Invoices on the Sales tab with payments applied. I did delete all the invoices because there was an option to do so. However, all the payments still show on the Sales tab and in Unapplied Payments account. When I click on one of the payments in the Sales tab, it opens ALL of them and shows them under a “Credits” heading and there is no option anywhere on the screen to delete any of these credits/payments. It appears it wants me to apply the credits/payments to an invoice, but they need to go away completely.

Does that make sense? How do I delete these?

Hello again, kito2020.

Thanks for providing detailed information about your concern. It was super helpful, and I feel like we are on the same page.

I have another workaround so you're able to delete the Unapplied Payment. Run the Unapplied Cash Payment account and remove it from there. 

Here's what you'll need to do:

1. In the left menu, click Accounting and go to the Chart of Accounts tab.
   
2. Type in Unapplied Cash Payment in the search bar. 
3. Under the Action column, hit Run report link. 
4. Set the Report period where the payments belong. 
5. Choose Transaction Type for the Group by filter. 
6. Tap Run report. 
7. Locate the payment and select the Payment link. 
8. On the Receive Payment window, hit the More button at the bottom. 
9. Select Delete, then Yes to confirm. 

You can repeat the steps 7-9 for other payments. 

For visual guidance, see below screenshots:

To give you information about how unapplied payments work in QuickBooks Online (QBO), take a look at these articles:

• What's Unapplied Cash Payment?
• Unapplied cash payment income on your profit and loss

Reach back out to me by commenting below if you have any questions concerning QuickBooks. I'm always here to help. Have a great day!

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Miriam:

How do I get rid of an over payment that keeps showing up as an unapplied payment?  I have applied the over payment to an open invoice, but despite my applying it, it's still deducting it on a different invoice that shows as being open?  This is frustrating me to no end because the payment should have been cleared out.  What do I do now?

Hello, jthomas2.

I also get frustrated when I have something that keeps appearing as an issue. I'll take it from here, and help you out in getting rid of the overpayment. I'll show you the step-by-step process on how it's done. 

First, let's remove the unapplied payment from the other invoice to put it back to the customer's balance (if you haven't done it yet). Here's how: 

1. Open the unapplied overpayment transaction. 
2. Uncheck the other open invoice.
3. Once done, click Save and close. 

Next, there are two separate ways to get rid of the overpayment. This depends on how it was handled. When you say cleared out, was it refunded back to the customer? If so, you'll want to create an expense or a check to remove it. Follow the steps in this article for a guide: Record a customer refund in QuickBooks Online.

If the overpayment wasn't refunded and you want to clear it, then you'll want to offset it using a journal entry. I'd recommend reaching out to an accountant before doing this to ensure your books are correct. 

First, create an offsetting account (usually an expense). Simply go to your Chart of Accounts, click the New button then set it as an Expense account. 

Next, create a journal entry: 

1. Click the + New button, then choose Journal entry.
2. Select Accounts Receivable on the first line. 
3. Under Debit, enter the overpayment amount.
4. Choose the offsetting expense account on the second line.
5. Add the same amount under the Credit column. 
6. Select the name of the customer under Name (first line). 
7. Hit Save and close.

Finally, link the journal entry with the unapplied payment: 

1. Click the + New button again, then select Receive payment.
2. Choose the name of the customer.
3. Check the journal entry under Outstanding transactions.
4. Do the same for the unapplied payment under Credits. 
5. Once done, click Save and close. 

This clears out the unapplied payment from the customer's profile and will zero out the balance. This won't touch the open invoice (which is what we want to avoid).

Need help managing your customers, account, vendors, and other tasks? Our articles are always available for reading. They contain guides, information and other helpful details. Check them out here.

Post a reply below if you have other questions or concerns for QuickBooks Online. The Community team and I will always have your back and be ready to help. 

I do want the over payment to be applied to the one invoice because on a past invoice they overpaid.  Instead of refunding the credit back to the customer, the customer chose to have it applied to the current open invoice.  Does that change the way this is handled?

Hi there, @jthomas2.

I'm here to ensure you're able to fix this transaction in QuickBooks Online.

You’re right in applying the credit to the customer's open invoice. If you turned on the Automatically apply credits feature in the system, it applies directly to the next invoice.

 However, if you have already created a credit memo, you can proceed in applying it to the invoice. Follow the steps below on how:

1. Click Sales from the left pane.
2. Select Customers and click the customer’s name.
3. Locate the invoice you want to apply the credit to and click Receive Payment.
4. Enter the necessary information on the Receive Payment window.
5. In the Outstanding Transactions section, make sure that the correct invoice is selected.
6. Click Save and close.

You can refer to this article to know how to enter and apply a credit memo in QuickBooks Online. Enter and apply credit memos and delayed credits in QuickBooks Online.

Please let me know if you have any questions. I’ll be here to help. Wishing you the best!

I've seen the delete option for undeposited funds through the Chart of Accounts, but when I clicked delete and got a message that the delete would create a credit I stopped.  I don't need a credit anywhere else, I simply need to remove the money in Accounts Receivable and Undeposited funds.  I made a Journal entry to record the money to the proper account, so it is there, but my year-end financial statements still show the account receivable and the undeposited funds.

Thanks for joining this thread, @mpzarr.

 As an insight, you can only remove the credit balance in accounts receivable by applying it to an invoice or edit the payment/overpayment for that specific amount.

 For additional reference, I've attached some helpful articles that you can check:

• Apply a credit from an overpayment
• How to link a deposit to an invoice

Let me know if you have further questions in managing your account. I'm always here to help. Have a great day!

I also did the Sync for Square thing a couple of months after opening my business in early 2022 and have a few thousands in extra sales in QB. Because of this I have undue extra tax, wrong numbers all over. I am just going to try to unlink Square with Quickbooks and try to delete whatever information I have just to try to get my numbers back on track. I never imagined linking these programs would create a nightmare.

Did this work for you? I have the same situation and don't want to delete a bunch of unapplied payments.