Hello, nonyanon. 

Thanks for hopping into this thread! Here are the steps to help your account add the PayPal fee by creating a deposit.  

Here's how: 

1. Click the +New button.
2. Select Bank Deposit.
3. On the Select the payments included in this deposit section, select the payment you recently entered.
4. Below the ACCOUNT column, select your PayPal or Bank Fees account.
5. Enter the amount of the processing fee. Say -3.
6. Press Save and close. 

I'm adding this article to learn more about deposits in QBO, How to Record Bank Deposits in QuickBooks Online.

For future task, here are articles you can read on how you can manage your bank deposits:

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

Additionally, Feel free to check out our articles if you need help familiarizing its features and processes.  

I'm ready to help you out again in managing your transactions in QuickBooks Online. Add your replies here or create a new thread and I'll be right there with you. Stay safe!

This is not correct because I do not have Paypal in my system as a Bank.  The deposit came into our books as $97. but the Invoice paid by client was $100.  If I make Bank Deposit of -$3, I would have to show the deposit as $100.

Please help with a work around because this Paypal payment is rare and we prefer not to bring in PayPal as a bank account into our books.  Unless I can bring in all of 2021 PayPal transactions - thus may I have instructions for that please? And would it be worth it with PayPal glitches.

OR is there a way I can create an invoice in QB as $100 and match it and then be able to add $97 as client payment and add the $3. as bank fee?

Thanks,

ny

EAA

I appreciate the details that you gave, @nonyanon.

Let me provide some clarifications about tracking your PayPal transactions in QuickBooks Online.

The steps shared by my peer above is the best way to handle your payment. This is to record the real happening on the invoice payment. You can use any expense account to hold the fee and clear it out after.

You may consider creating a bank fee account to track your bank fees in the system. You can zero out the unnecessary entries in this account afterward. This can keep your records accurate.

You can follow these steps below to create a Bank Charges account:

1. Go to Accounting from the left menu.
2. Choose Chart of Accounts.
3. Click New.
4. In the Account dialog, create an Expense account for Bank Charges, and give it a name, e.g Bank Charges or Bank Fees.
5. Select Save and close.

You can refer to our guide for your convenience: Add accounts in QuickBooks Online.

Once done you can now deposit the payments by following the steps presented above. The negative figure that you'll going to deduct on the deposit can be cleared using a journal entry. 

However, to ensure that best course of action for your business, you may consider reaching out to your accountant. 

I'm also adding here some recourses that you can use in reconciling and categorizing you bank transactions in QuickBooks Online:

• Learn what to review so you can start reconciling
• Match and categorize all of your downloaded transactions

I'll be right here to provide continued support if you need more help with your bank transactions. Have a nice day!