Link Square transaction to bank deposit and then invoice.

I'll guide you in handling that, JAMESB4.

Take note that you'll only have to match the downloaded Square transaction after you apply the deposit entry as an invoice payment. This way, your books always reflect your real-life business transactions.

Moreover, It won't cause any issues if you choose not to link the Square transaction. You'll can just exclude it from the Banking page and then manually clear the payment in your bank register. Here's how: 

1. Go to the Accounting menu.
2. Select the Chart of accounts tab.
3. Find the account that has the reconciled transaction, then select View register.
4. Locate the appropriate transaction, then select it to expand the view.
5. In the Checkmark column, keep clicking the box until you see a letter "C". This marks the transaction as cleared.
6. Click Save, then close the register.

I'm also adding these articles to help manage your bank transactions and keep your QuickBooks balance accurate:

• Categorize and match online bank transactions
• Reconcile an account

Feel welcome to reach out to me again with any concerns or questions you may have. The Community always has your back.

I have found a flaw with applying the deposit entry as an invoice payment before matching the downloaded Square transaction, it leaves a difference from the Square fees.

Also, if I don't link the Square transaction to the bank deposit will I have documentation of the fees I have to pay for the Square transactions?

I am using the Square connect app with my Quickbooks and am questioning would it make more sense to disconnect the app and just using the deposits in my bank account to close invoices along with documenting the Square fees.

Thanks

Hello, JAMESB4. 

Disconnecting the Square app won't affect your bank feeds. However, it won't sync your Square sales transactions including Square fees, tips, refunds, and more.  

To prevent duplicate transactions, please do not do any of the following: 

• Run multiple integration methods, at the same time, to import information from Square.
• "Add" your bank feed transactions for your Square account instead of "Match" them.
• Import transactions by using different methods of connecting to QuickBooks for dates that have already been imported.
• Invoke different methods of connecting QuickBooks to Square at the same time.
• Pull transactions for overlapping dates.

Feel free to read this article about sync with Square FAQ's: Sync with Square Hub. 

I'll be here to help you out if you have any other concerns with QuickBooks. Have a great rest of your day. Stay safe!