@Deb143 

Do you need to reconcile Braintree transactions into your QB Desktop file or else?

What if there are two invoices combined and a fee removed?  I get a double the received amount showing the the bank account.

Thank you for joining the thread, @22JPG.

I'd love to help you with your concern about combined invoices and a removed fee. But can you please provide more information about the two invoices you combined? Also, can you share a screenshot of it? Any additional details would help us provide the best resolution on this matter.

Please know you can continue to reach me here with your additional questions. I'll be standing by for your response.

Nevermind.  I've figured it out. 

Thanks!

ZelayaCompanies,

You just saved me!  I've been searching for how to do just this for a very long time!  CPA couldn't help.  

One small adjustment to your recommendation:  I had to manually adjust the amount received to INCLUDE the credit card/paypal fees to then DEDUCT them as a negative charge as an expense.  Worked!  Thank you!

Quickbooks Desktop is easy. (im still trying to figure it out for QBO)

When in Desktop, go to banking receive payment. Select your customer, date, amount of deposit and reference.  Select the invoice(s) being paid. Make sure your invoice is "highlighted" and select Discount/Credit on the top. Make sure yo are on the discount tab. Enter in the amount of the fees and select the expense account (example credit card fees) that you want to the expense recorded in.   If you have mulitple invoices, you can apply a portion of "discount" to the invoices by repeating the steps, or you can apply the entire discount to 1 invoice. Now all your invoices should be paid in full in A/R. And when you go to do your bank reconciliation, the actual amount deposited in the bank will show up in the deposits section.  (not a credit and a debit that you have to manually net to get the total deposit)

When adding this line to the deposit, should the line item be income? Just, the negative makes it like negative income in a way? 

I'm having this same issue. I put the account on the receive payment as undeposited funds, then in the banking feed I had the deposit come through for less. I clicked match and found the Payment, and then slid the button over at the bottom to "Resolve" and added a line on which I added a new account "Bill.com Fees" and placed that account under Services (Income). Does that work?

Some banks tack on processing and service fees, @kcalvert1245. 

In QuickBooks, don't make changes to the initial transactions. As an alternative, incorporate the fee while working on the bank deposit window:

1. Go to the Add funds to this deposit section.
2. Enter the fee as a line item.
3. Choose who the fee was from (for example, the bank charging you).
4. Select Bank Charges from the Account ▼ dropdown.
5. Enter the amount fee as a negative number. For example, if the fee was US $.50, enter –.50.
6. Review the deposit total with the bank fee.
7. Click Save and Close or Save and New.

You can read this article for the detailed steps in making bank deposits: Record and make bank deposits in QuickBooks Online. Scroll down to the Include bank or processing fees section.

I'm also adding these links to guide you on how to categorize your transactions and reconcile your account:

• Categorize and match online bank transactions in QuickBooks Online.
• Reconcile an account in QuickBooks Online.

Don't hesitate to get back to us if you need additional assistance in making bank deposits. I'm always here to help. Have a great day.

How do I get to the receivrpayment screen? I only receive personal checks for payment

Hello, DebbieK61.

I can walk you through the steps of getting to the receive payment screen. 

To be clear, are you attempting to apply the personal check as payment to your customer's open invoice? If this is the case, you can deposit the check first, then use the Account Receivable (AR) account to link it to their invoice.

Here's how:

1. Click the + New icon.
2. Select Bank deposit.
3. Go to the Add funds to this deposit section.
4. Choose the customer who pays you with a personal check in the Received From column.
5. Select Account Receivable from the Account field, then choose a check from the Payment Method area and enter the amount.
6. Once done, hit Save and close.

After that, apply the deposit as payment to the open invoice.

Here's how:

1. Click the + New icon.
2. Select Receive payment.
3. Choose the correct customer from the Customer dropdown.
4. Ensure to select the correct invoice under the Outstanding Transaction section and choose the deposit you created for the personal check in the Credits section.
5. Once done, hit Save and close.

Check out this article for more insights: Record invoice payments in QuickBooks Online.

I've included the following helpful resources below if you need help with customer credits or overpayment for future reference:

• Record a customer refund in QuickBooks Online
• Handle a customer credit or overpayment in QuickBooks Online

Don't hesitate to post again if you need further assistance recording payments in QuickBooks. I'll be around to help you.

Hey @JenoP 
I need help in my scenario I hope you can help me.

I have an invoice of $100 and the payment of $104 ($4 charge to customer stripe processing fee) in my software. Now I'm just syncing the Net payment of an invoice. I do not want to add a Line item.
e.x:
I received from user $100 + $4 (stripe processing fee) => in QuickBooks the invoice is $100 and I pushed the payment $100. so I want to sync the $4 correctly.

I'm following the way to record the payment for invoice and Sales Receipt for the "Merchant Fee charged to Client (other income A/c).

Does any other way so I can follow the approach? For tips Sync I'm syncing the Tip to Undistributed Tips account by credit the Undistributed Tips & debit the Undeposited Funds.

I just want to record the processing fee for the Report without affecting user invoice & customer balance.

Hello there, @Brilliant16.

I'll share insights on how you can record sales and fees in QuickBooks Online (QBO) to keep your income data accurate.

What happens to your real-life business should match with the ones in QuickBooks. When there's a processing fee, you'll need to include it (as a line item) in your invoice to record it properly. This ensures your books are correct and track sales and income accordingly.

Since you don't want it to affect your customer's invoice and balance, you can create a journal entry (as directed by my colleagues). However, I'd recommend consulting your accountant to guide you through the right process and selecting the appropriate accounts.

Once everything is all set, you may want to track your sales and income transactions by pulling up customer transaction reports (for example, Sales by Customer or Income by Customer). To do this, go to the Reports menu's Standard tab and search for the one you need.

If you have other concerns about managing invoices and payment transactions in QBO, please don't hesitate to let me know in the comments below. I'll gladly help. Take care, and I wish you continued success, @Brilliant16.

Yes I understand about journal entry. What if I Credit the Merchant Fee charged to client (other income) and  Debit the Undeposited Funds? or I've to follow this approach only Do I've to Debit the Expense and Credit the Bank account? 

Now my customer shows a Negative Balance for the discounted amount that was posted to credit card processing fee