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:
- Go to Accounting from the left menu.
- Choose Chart of Accounts.
- Click New.
- In the Account dialog, create an Expense account for Bank Charges, and give it a name, e.g Bank Charges or Bank Fees.
- 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:
I'll be right here to provide continued support if you need more help with your bank transactions. Have a nice day!
