Square integration creating duplicate entries

Thank you for the detailed information, GGLLC. I'll ensure to guide you in handling the transactions with different amounts in QuickBooks Online (QBO).

In this case, the payment amount on the bank register won't match the deposit amount in QBO since you received the payment from third-party merchant services, and a bank service fee is deducted from the payment. That's why, the amount imported from the Square is only $104.99 and doesn't match the invoice amount you've created.

To fix this, you can enter the bank service fee amount directly into the register and add it as a negative amount on the Bank Deposits screen. This way, the register balance matches the bank statement balance. 

To enter the amount in the register:

1. Go to the Transactions menu, and choose Chart of Accounts.
2. Select the right account, and then click View Register from the Action column.
3. Add the bank service fee, and then click Save.

Once added, you can now enter it as a negative amount. 

Here's how:

1. Click on the + New button and select Receive Payments.
2. Select the checkbox next to the invoice you would like the payment to be applied to.
3. Set the Undeposited funds as the deposit to the account.
4. Enter all the necessary information.
5. Then, click Save and Close to record the transaction.

Then, it's time to create a bank deposit:

1. Click the + New button, and select Bank Deposits. 
2. Place a checkmark to select the payment you want to deposit from the Select the payments included in this deposit section.
3. From the Add other funds to this deposit section, enter the amount of the bank service fee charged by the Square app as a negative amount.
4. From the Account section, select the Expense account you usually use in tracking bank fees.
5. Verify that the deposit amount is correct.
6. Then hit Save and Close to record the transaction.

For reference, you can check out this article: Enter a bank service fee using a third-party merchant service in QuickBooks Online.

For future reference in managing your bank transactions and reconciling accounts in QuickBooks, you can visit these handy articles: 

• Categorize online bank transactions in QuickBooks Online
• Reconcile an account in QuickBooks Online

Feel free to reply to this thread if you have questions about handling your transactions. I'm still around to help you.

Ok.  This is not working properly. 

1.  I do the "receive payment" for the invoice and apply it to Undeposited funds

2.  I create the bank register, check the invoice, apply the CC fee as a negative amount and apply it to the Bank Fees & Service Charge account

3.  Top left says "Account" with a drop down menu.  My only options are my CapitalOne Checking, QB Cash or QB Checking.  Since I do not use the QB bank accounts b/c Green Dot has given me too many problems, the CapitalOne Checking one is selected.  There are no other options besides these 3.

4.  After (2), I then click Save and Close and now the entire adjusted payment is applied to the register for my CapitalOne Checking account.  Since this is now applied, and the original deposit from Square was applied via the integration, I now have 2 of the exact same deposits into the checking and the amount is now duplicated.

This is insane how difficult this is.  I've had so many issues with QB already and I've only been using it for 2 months.  This is getting dangerously close to not worth it.  This is supposed to be easy.

What is your next fix here?

I know how you're feeling about the square integration creating duplicate entries, @GGLLC.

Let me chime in and clarify to resolve the duplicate entries in QuickBooks Online (QBO).

To clarify, what we can do is delete or remove the payment received from an invoice that was deposited to Undeposited Funds. In your case, as you deposited it in a Capital One checking account, the match will not be successful, since the Square Integration transaction should be the one to match your bank deposit record in QuickBooks.

Once done, you'll need to link the invoice directly to the Square Transaction by selecting the app transaction and using the Find Match button. Then, turn on the Resolve Difference option to allocate the 3.89 to a specific expense or income account. However, if you're unsure about where to allocate the fee, it would be best to consult your accountant for more precise information.

To resolve the difference, follow these steps:

1. Go to the left navigation panel, and select Transactions.
2. Select the App Transactions, locate the invoice transaction, and click it, then use the Find match button.
3. Filter the date to get accurate matches. then select the transactions to match and then click the Resolve difference.
4. Select the Payee and the Category.
5. Review it and then select Match.

Additionally, I recommend reading this article to guide you in reviewing your accounts in QuickBooks to ensure that they match your bank and credit card statements: Reconcile an account

If you have any concerns about duplicate entries, please tag me in the comment section, @GGLLC. I'll assist you in any way possible.