I agree, and while the process does work, the level of effort for each transaction is ridiculous.  At this point I'm not sure if the problem is QBO, the Square integration, or both.  What I would like to see is the invoice section have an option to select Square instead of Quickbooks Payments.  I would like to see seamless matching of the invoice, sales receipt, and deposit without duplication and workarounds  Very frustrating.

What about the credit fees, how do we post them after the Square payment is posted?

Managing fees after a Square payment is posted in QuickBooks Online can be a bit tricky, barneysny06. No worries, we've got you covered. In this guide, we'll walk you through each step to ensure Square fees are accurately recorded in QuickBooks Online, making your financial tracking a breeze.

You can create an expense transaction to record the fees, but before doing so, let's create an expense account for the fees first. Here's how:

1. Go to the Gear icon at the top of your QuickBooks Online (QBO) account.
2. Choose Chart of accounts.
3. Click New.
4. Enter the Account name.
5. Set the Account Type to Expenses and the Detail Type to Bank Charges.
6. Select Save.

To record the fees, follow these steps:

1. In the left menu, click the + New button and select Expense.
2. Leave the Payee field blank.
3. Under the Category column, select the expense account you created for Square Fees.
4. Enter the amount of the fee under the Amount column and save the transaction.

After that, match the deposit to the corresponding customer payment.

For your continued success and ease in managing your accounts, I highly recommend bookmarking this insightful guide: Reconcile an account in QuickBooks Online. This article not only walks you through the best practices but also offers invaluable tips for tackling any challenges you may encounter during the reconciliation process.

We truly value your financial clarity, and we're committed to making your experience as effortless as possible, barneysny06. Should you have any further questions or need additional support, please don't hesitate to get in touch. We're here to assist you in navigating any challenges.

With respect, this is answer is absolute nonsense.  Square and QBO sync very nicely until you want to use invoicing.  QBO's answer is to do everything manually?  On numerous transactions with invoices?  Absolutely not!  I've read through three years of these threads and this problem is still not resolved with a realistic solution.  This is a major software feature issue.  PS. No, I'm not switching to QB payments to "fix" the problem.  

Assuming you have your bank account and the Square integration app setup in QBO, the credit card fees are automatically accounted for when add and match the transaction.  It's actually works quite well.  Everything blows up when you use QBO invoicing. You end up with duplicate payment entries and missing credit card processing fees that you manually have to sort through.  It is not a viable process.

@jam1251 ...I like your solution. I've recently switched to QB as well. Would you mind sharing your step by step guide for manually posting Square payments to existing invoices. I'm so lost. Thank you