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Level 1

Credit card transaction fees

I use QuickBooks online and Gopayment. I received my first credit card payment. The app recognized the transaction fee, but then the total amount was deposited into my bank account, the fee was not taken out before depositing in my account. Is this a mistake? I figured the transaction fee would be taken from the total and then what’s left be deposited into my bank account. 

QuickBooks Team

Credit card transaction fees

I’m happy to see you in the Community, tcsmitty.

QuickBooks groups the entire customer payments processed for that day into a bank deposit. It records only one bank deposit per day.

However, the online program separates payments and fees so you get all the details. They appear as separate transactions on your bank statements.

Since the transaction fee is not taken out, let’s manually enter it in your company. Let me help and guide you to accomplish this task.


  1. Open the invoice for the customer you’re working on.
  2. Click an empty line below the Product/Service column.
  3. Select Add new from the drop-down and choose Service.
  4. Fill in the fields with the correct information.
  5. Enter the description of the transaction fee in the Name field.
  6. Type a negative figure in the Amount USD column.
  7. Click Save and close.


Once done, add the bank to your chart of accounts. This way, all deposits, and fees are automatically tracked to the account. Check out this article for the step-by-step process. It includes information on how the program records the fee on the account: Record payments deposits and fees in QuickBooks Online.

For future reference, these resources contain answers to frequently asked questions about the Payments feature. From there, you’ll find instructions on how to configure your chart of accounts to track fees.



If there's anything else you need help with QuickBooks, feel free to leave a comment. Thanks and have a nice day!

Level 1

Credit card transaction fees

Thank you for your response.  Let me clarify my issue: It's not an issue of recording the transactions in quickbooks.  The deposit to my bank account was for the full amount.

I charged a customer for $6,002.49.  The fee is $204.33.  But the amount deposited into my bank account was fore the total $6,002.49.  Why didn't quickbooks take their fee? 

Level 1

Credit card transaction fees

Thank you for your response.  Let me clarify my issue:
It is not a problem of recording the transaction in quickbooks.  The money deposited into my bank account was for the entire amount charged to the customer- there was no fee taken out. 

I charged my customer $6,002.49, the fees amounted to $204.33.  The amount deposited into my bank account was for the full amount of $6,002.49.  Why didn't quickbooks take out their fee?

QuickBooks Team

Credit card transaction fees

Thanks for getting back here, tcsmitty.


The fees will depend on how you processed the payment. If the amount was not taken out, contacting our Merchant Services Team is the best thing to do here. They can help review your account and confirm the charge. 


You can click on the Chat with us link here: Contact Payments.


I'm also adding these articles for more details about QuickBooks Payments:



Please feel free to reply on this thread if there's anything else you need. Me and my colleagues are always here to provide instructions. Have a great day!

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