We're a new business, and new to Square and Quickbooks. The fee for Square is not being recorded automatically in QB. Do I do a journal entry for the fee?

Hi there, @drgrimes5.

Thank you for choosing QuickBooks, and welcome to the Community space! I'm here to assist you with your concern about adding Square fees in QuickBooks Online.

There's a process to account for the fees in the system. We recommend creating an expense account to track these amounts from Square.

Here's how:

1. Go to Bookkeeping and select Chart of accounts. 
2. Select New.
3. In the Account dialogue, create an Expense account for Bank Charges, and name it Bank Fees.
4. Select Save and close.

Once done, the next step is to resolve the difference when matching transactions. You can use this if you received less than the due amount on the invoice because of Square fees, and you need to record this from the Bank Feed.

Please follow these steps:

1. Go to Bookkeeping, select Transactions, then select Bank transactions.
2. On the Bank and Credit Cards page, make sure you have selected the Bank Account  with the transaction.
3. Locate and select the relevant Transaction on the For Review tab.
4. Select Find Match.
5. In the Match transactions window, select the checkbox of the appropriate Invoice.
6. Select Resolve Difference to open the Add resolving transactions fields.
7. Select Add new transaction.
8. From the drop-down list in the Category field, select the Bank Fees expense account you created.
9. Enter the Amount of the bank fee.
10. Select Save and close.

Alternatively, you can use the Journal Entry feature to record the fees. However, It would be best to seek expert advice from an accountant regarding the accounts to affect.

Also, payment processing companies like Square usually add service charges and processing fees. I've attached a link you can visit to learn how to add fees to transactions added to QuickBooks manually (scroll down to (Include bank or processing fees): Record and make bank deposits in QuickBooks Online.

Drop me a comment if you need more help adding the Square fees or navigating QuickBooks. The Community and I will be sure to guide you through this thread. Take care.

@drgrimes5 

Another option, you can utilize a 3rd party app to reconcile your Square transactions easily into QBO.