How do I document the Stripe/Square Fees into QuickBooks (Online) to where it won't mess up the balance when you go to reconcile?

Hi @treasurer63,

Invoices and their corresponding payments created from Square are automatically imported to your QuickBooks Online (QBO), given that you've synced Square to QBO.

As for those payments, the bank fees are already accounted for. If you need to track these in QBO, you'll have to exclude the deposits coming from Square, and create it manually within the system.

Here's how:

1. Open the invoice created from Square.
2. Click the Receive payment button.
3. Input the entire amount of the invoice on the Amount received field.

Next, we'll need to create an expense account to track these bank fees. Here's how:

1. Click the Accounting tab.
2. Tap the New button.
3. Set the Account Type to Expenses.
4. Set the Detail Type to Bank Charges.
5. Enter the name you want on the Name field.
6. Hit Save and close when done.

You can create an expense transaction at this point. Follow these steps:

1. Click the + New button.
2. Select Expense.
3. You can leave the Payee field blank.
4. Under the Category column, select the expense account created earlier. 
5. Enter the bank fee under the Amount column.
6. Press Save and close when you're done.

Doing all these steps, you've recorded that you received the full amount on any given invoice, as well as recording the bank fees as an expense, keeping your bank balance accurate. 

Learn more of the default accounts used by Square in this article: Sync with Square - Default Accounts and Names.

If you have other questions in mind, post them below, and I'll make sure to get back to you.