How to record payment for deposits that don't match

Welcome to the Community, @EnaWM. Let me help you match the customer payments and invoices in QuickBooks Online (QBO).

The service charge or fees must be manually added to the invoices in order to match it to the customer's payment.

Please follow the steps listed below to add a service charge to an invoice transaction:

Step 1: Create a service charge item.

1. Go to Settings ⚙, then Products and services.
2. Select New, then click Service.
3. In the Name field, enter a name for the service.
4. (Optional) From the Category ▼ dropdown, choose the category that best describes the fee. Find out more about item categories.
5. (Optional) Fill out the rest of the fields.
6. Once done, hit Save and close.

Step 2: Add a service charge to invoices.

1. Go to the Sales menu, then the Customers tab.
2. Find and open the customer's invoice.
3. From the Product/Service ▼ dropdown, choose the service fee you created.
4. (Optional) In the Amount field, enter the amount of the service fee.
5. (Optional) In the Message on invoice section, add a note about the fee.
6. Once done, hit Save and close.

If you added the service charge to a deposit transaction, you can follow the procedure in this article: Enter a bank service fee while using a third-party merchant service.

I've also included the following resource, which you can read for your upcoming task about assessing your accounts in QuickBooks Online: Reconcile an account in QuickBooks Online.

If you have other QuickBooks-related concerns, please don't hesitate to visit us again in the Community. We'd love to help you again. Stay safe, and have a great day ahead!

Thanks for explaining it further, @EnaWM. We're glad to help you handle the service fee that has been charged to your client and record the payment in QuickBooks Online (QBO).

We understand the importance of keeping track of the payments and other transactions in QBO to ensure the accuracy of your books. In this case, we recommend recording the invoice and payment without bank fees first and then creating a deposit from that payment, where you can deduct the bank fees. We'll show you the process below:

To record the invoice and payment:

1. Click on the +New button.
2. Select the Receive Payments.
3. Enter all the payment information.
4. From the Deposit to section, choose the Undeposited funds as the deposit to account.
5. Then click Save and close.

After that, we can create a deposit to combine transactions in QuickBooks. See the steps below:

1. Select the +New button.
2. Choose Bank Deposit.
3. From the Account dropdown, choose the account you want to put the money into.
4. Tick the checkbox for each transaction you want to combine.
5. From the Add funds to this deposit section, enter the amount of the bank service fee charged by the credit card company as a negative amount.
6. On the Account section, select the Expense account you usually use in tracking bank fees.
7. Ensure the deposit amount is correct.
8. Then click Save and close.

Please check this article for reference: Record and make bank deposits in QuickBooks Online.

If you would like to reconcile your account, here are a few additional articles to help you accomplish a successful reconciliation:

• Reconcile an Account in QuickBooks Online
• Learn the reconcile workflow in QuickBooks

Please let me know in the comment section for more details about managing bank deposits or any other QuickBooks-related concerns. We'll always be here to assist you. Take care always, @EnaWM!