thread Re: Square Fees not showing up correctly in Quickbooks integration in Payments Troubleshooting

Square Fees not showing up correctly in Quickbooks integration

TheFunkyPIta — Sat, 20 Sep 2025 11:02:42 GMT

Hi, I am new to Quickbooks. I just linked my Square account with the Connect by Quickbooks App. I also have a Square Savings account in which I automatically save 15% of my credit card sales. I have found that when the deposits are recorded in Quickbooks the Square fees that are entered include the automatic amount that is going into my savings account. I have to manually go into each transaction and separate the transaction.

For example in my last deposit I had $1.96 in Square Fees, and $11.15 go into my Square Savings Account. In Quickbooks, however, it added these two numbers together and showed that I had $13.11 in Square Fees. I have to manually go in and separate these transactions. Is there a way for it to automatically categorize it correctly in Quickbooks?

Thanks for your help!

Re: Square Fees not showing up correctly in Quickbooks integration

Candlestore — Fri, 18 Feb 2022 15:49:52 GMT

What type of QuickBooks account do you have, online or desktop version?

A little more information would be helpful.

I use the desktop version and I have "mapping" I have to do for my QuickBooks to know how to handle different transactions for fees, taxes, items etc.

If you are using online I do not know if there is a mapping for you to do with Squares integration.

I have read of stories where the financials get transferred over online but not all the items and inventory. Since a Square Loan is a loan not a sale, the transfer process may not be set right for that type of transaction integration. I also read in this forum of people asking Square about the integration and asked QuickBooks about it and both seem to point the fingers to the other.

I use a program that is called Transaction Pro Importer (TPI)

QuickBooks Desktop is $199 for the importer 1 time or $299 for Importer/Exporter/Deleter Pro also 1 time

QuickBooks online version is $10, $30 or $50 a month depending on your needs.

website here: https://www.transactionpro.com/pricing

I just looked at TPI, it maps Journal entries which is how you may have to do the loan but I am not sure since currently I do not have a Loan from Square and do not have a loan to test with.

Re: Square Fees not showing up correctly in Quickbooks integration

blossombird — Fri, 12 Aug 2022 12:11:06 GMT

Hello, I'm looking for answers to the exact same issue. Have you found a solution?

Re: Square Fees not showing up correctly in Quickbooks integration

empanolabiloxi — Fri, 24 Feb 2023 00:01:21 GMT

@TheFunkyPIta Did you ever get a resolution to this? I'm having the exact same issue. Ridiculously frustrating!

Re: Square Fees not showing up correctly in Quickbooks integration

Candlestore — Fri, 24 Feb 2023 15:45:53 GMT

@empanolabiloxi ;

Since I see the original poster has the Connect by Quickbooks app, if you have the same app you would need to contact the app manufacturer to see how to resolve this. From what I have been seeing in these forums both QuickBooks and Square keep pointing fingers at each other. QuickBooks says they do not get the information Correctly, and Square says Quickbooks App does not separate it correctly. So my suggestion is to contact the maker of the integration you are using and see if they have come up with a resolution.