What is the correct way to record service fees on a payment from a client that are generated from their bank, not ours?

I'm here to help you to record the bank fee, jmaurer1.

Yes, it's important to track the service fee even if it is not charged by your bank. To do so, you can enter the fee as a negative amount on the Bank Deposit page when you make the payment deposit.

Beforehand, let's record the 1000 invoice payment you receive from your client. Here's how:

1. From the QuickBooks Home page or the Customers menu, select Receive Payment.
2. In the Received From drop-down, select the customer's name.
3. Enter the Amount received.
4. Add the correct date, then choose the Undeposited Funds account as the Payment method.
5. Select the invoice or invoices you'd like to pay.
6. Click Save & Close.

Once done, you can now deduct the fee from the payment. I'll show you how:

1. Go to the Banking menu and select Make Deposits.
2. In the Payments to Deposit window, select the $1000 payment, then select OK.
3. From the Make Deposits window, select the account you want to put the deposit into from the Deposit to dropdown.
4. Add the fee on the second line as a negative amount.
5. Select the correct account.
6. Enter the other details needed, then click Save & Close.

Please note that when assigning fees, you can select an expense account. However, it would be best to consult with your accountant to ensure that the fee is tracked accurately.

Additionally, I've added these articles that'll help you review your transactions and ensure they match your bank statements:

• Categorize Transactions in QuickBooks Desktop
• Reconcile an Account in QuickBooks Desktop

We always have your back. Let us know if you have further questions about QuickBooks and managing invoices. 

I have the same situation but when I recorded the payment I recorded what was received (amount minus the wire charge from their end) which left a balance on the invoice. Now I have a number of invoices with a $5 balance. How do I "fix" it to have the invoice reflect a paid balance? I don't want QB to reflect the total amount of the invoice as income because the actual amount billed versus the amount received are different. (I E. Invoiced $900 but actually received only $895).

Thank you for sharing your concern here in the Community, @assuroptum. Let me provide detailed information to tag your invoice as paid in QuickBooks Desktop (QBDT).

In this situation, your invoice shows an outstanding amount of $5. You have options to either label the invoice as paid by using the credit memo or apply it as a discount or credit. I've covered some steps below to guide you through this process.

1.  Go to the Customers tab and click on Create credit memo/refund.

2.  Make sure that it has the correct customer or customer job applied.

3. Select an item, then enter the balance amount.

4.  Click Save and Close, then choose Apply to an Invoice.

5.  Select which invoice you are going to apply for credit by checking the box on the left side of the date column.

6.  Confirm the transaction by clicking Done.

An alternative way is to use the Receive Payments option. Here's how:

1. On the dashboard, click on the Receive Payments icon.
2. In the Customer Payment window, select the Discount & Credits button.
3. Click on the Discount tab, under the amount of discount, and type in the balance amount.
4. After hitting Done, select Save and Close.

Apart from this, verify if the invoice is marked as paid. You may refer to this article for additional details: Record an Invoice payment.

Furthermore, let me share this article to learn how to set up and use progress invoicing in QuickBooks Desktop: Set up and send progress invoices

Keep me posted if you have further questions about your invoices. I’ll be around to back you up. Have a good day ahead.

How will applying the $5 unpaid amount as a discount or credit affect my income when tax time rolls around? We invoiced for the full amount but did not receive full payment because there was a fee tacked on on their end.  Our income should reflect that although we invoiced the full amount, the full amount was not received. My invoices and my check register do not match.

Hi there, assuroptum.

I appreciate you for coming back to the thread to add extra clarification about your concern. However, we aim to deliver customer satisfaction at all times and address an issue as soon as possible. With this, may I ask for more clarification if the $900 you indicated includes the tax? Or is this the original transaction amount, excluding taxes? Could you please also include a screenshot of your invoice? I appreciate any additional information so that I can present accurate information. 

For now, you may refer to this article to see details on how QBDT allows you to manage and track your Customer Balances effectively: Manage accounts receivables in QuickBooks Desktop using Financial Exchange.

Don't hesitate to click the Reply button below and add extra details about your concern. I'm always around to help you, assuroptum.

I am unable to screen shot the invoice for confidentiality reasons. The invoice is for services and no taxes are included in the invoices as they only include billable time.

Let me explain how applying unpaid amounts as discounts or credits can affect your income during tax time, @assuroptum.

Unpaid amounts in invoices can impact income accounting differently depending on the financial arrangement and accounting method. Cash-basis taxpayers can't write off unpaid invoices, while accrual-basis taxpayers can write them off as bad debt if uncollectible.

Additionally, when a customer pays less than the invoiced amount due to a bank fee or any other reason, your actual income will be less than the invoiced amount. To accurately reflect this, you'll need to record the payment and apply the bank fee as a negative amount. 

First, ensure you've selected the appropriate accounts. You can choose an Account Receivable (A/R) and an Expense account. When recording the bank fee, you can choose an Expense account and record it as a negative amount. The remaining amount will be under the Account Receivable account. 

Here's how:

1. Go to the Banking menu, then select Use Register.
2. Choose the Account in which you made the deposit.
3. Click the deposit.
4. Select an Account Receivable (A/R) and an Expense account.
5. Click Save & Close, and select Yes.

Then, you can apply the credits. You can follow these steps:

1. Go to the Customers menu, then choose Receive Payment.
2. On the Received From dropdown, select a customer.
3. Click Apply Credits.
4. Tick the box to apply for the credit, then select Done.
5. Hit Save & Close.

In case you accidentally apply a credit to an invoice or bill, you can remove it by following the steps in this article: Remove or unapply a credit from an invoice or bill.

We're still ready to back you up if you have further concerns with applying discounts or credits on invoices. Feel free to leave a comment below.