Hi there, @deblois. I'm here to help you assign a payment from the Square app to the invoice in QuickBooks Online (QBO). You can follow the steps I'll share below.

Firstly, we'll have to add the transactions from the Square app into the system. Once done, please know that it will create a sales receipt and a deposit.

Then, we can go to the Receive Payment section to apply a payment for the invoice you've created and send it to Payments to Deposit. To do so, here's how:

1. Head to + New, then select Receive Payment.
2. Select the Customer from the dropdown, then ensure you've selected Payment to deposit in the Deposit To dropdown.
3. In the Outstanding Transactions section, choose the correct invoice.
4. Hit Save and close.

Once done, we can go to Bank Deposit to record the payment you've recently created. Please follow the steps I'll share below.

1. Click the + New button and select Bank deposit.
2. Choose the bank account in the Account field and enter the Date.
3. Under Select the payments included in this deposit section, check the invoice payment you've newly created. Uncheck the sales receipt created when you've added the entries from your Square app.
4. Hit Save and Close.

You can check this article for reference: Record and make Bank Deposits in QuickBooks Online.

Afterward, we can delete the sales receipt created to match the deposit and payment in your bank feeds.

Additionally, you can check out these articles for future use if you need help handling your bank feeds:

• Categorize and match online bank transactions in QuickBooks Online
• Reconcile an account in QuickBooks Online.

Should you have other questions about assigning payments to an invoice? Feel free to reply to this post.

Hi ,

I did the first step to add the transaction from the Square app to Quickbooks.

I did the second step to Receive payment.

I did the third step to go to Bank deposit and select the payment include in this deposit.

After that I have a double sale from the same transaction and double deposit from the sale .

You mentioned to Uncheck the sale receipt created when I add the entries from my square app…and we can deleted the sale receipt created to match the deposit and payment…for those operations Quickbooks doesn’t allow to delete the sale receipt without cancelled the deposit.

Also I uncheck the sales receipt , it reduce the bank account but add the amount to undeposit funds , instead of reduce the sale amount .

Then I am still with my problem …

Hi ,

I did the first step to add the transaction from the Square app to Quickbooks.

I did the second step to Receive payment.

I did the third step to go to Bank deposit and select the payment include in this deposit.

After that I have a double sale from the same transaction and double deposit from the sale .

You mentioned to Uncheck the sale receipt created when I add the entries from my square app…and we can deleted the sale receipt created to match the deposit and payment…for those operations Quickbooks doesn’t allow to delete the sale receipt without cancelled the deposit.

Also I uncheck the sales receipt , it reduce the bank account but add the amount to undeposit funds , instead of reduce the sale amount .

Then I am still with my problem …

Thanks for coming back to this thread, @deblois. I appreciate you for following the steps provided by my colleague. 

It appears you've encountered a restriction when deleting the sales receipt. This happens when the Sales Receipt from the Square transaction you've added is still linked to the Deposit. I'm here to help provide further clarifications and steps in applying the Square payment to an invoice in QuickBooks Online (QBO).

You're on the right path of recording the invoice payment in QBO. Since adding a Square transaction from the App transactions page creates a Sales Receipt and Deposit record in QBO, we'll need to edit the Deposit to unlink the Sales Receipt and link it to the recorded invoice payment as the next step. You can follow this process:

1. Click on the Gear icon in the upper right corner.
2. Select Chart of accounts.
3. Find the bank account where the Square transactions are added. Then, select View register.
4. Find the corresponding deposit transaction at issue. To help in this task, click the Funnel icon and choose Deposit from the Transaction type drop-down list.
   
5. Select the transaction at issue. Then, hit Edit.
   
6. Uncheck the sales receipt linked and place a checkmark for the invoice payment.
7. Hit Save and close.
   

Then, you can now proceed with deleting the sales receipt. I've added a screenshot for a visual guide.

For future reference, let me add this article about reconciling accounts in QBO: Reconcile an account in QuickBooks Online.

We'll be here in the Community if you have further questions about applying a Square payment to an invoice in QBO. We'll do our best to assist. Take care.