I am syncing with Shopify and using a clearing account to track deposits. How do I show payment received for invoices sent from Shopify without duplicating?

Hello there, m-spurgeon. It's great to have you here in the Community!

To prevent receiving duplicate payments, you will need to manually create an invoice in QuickBooks Online (QBO) to record the payment.

Here are the steps you need to follow:

1. Click on the + New button and select Invoice.
2. Select the name of the customer.
3. Enter the information, then select Save and close or Save and send.

Once done, check the deposit in the clearing account and ensure the entries are posted to your Account Receivable.

 Let me walk you through the steps:

1. Go to the Gear icon and select Chart of Accounts.
2. Look for the clearing account and View register.
3. Locate and select the transaction.
4. Make sure the affected account is Account Receivable. Otherwise, change the category, then save the changes.

After completing the steps above, link the deposit and the invoices through the received payment feature. Lastly, match them to complete the process.

You can open this article to see various details on how to add and match transactions in the program: Categorize online bank transactions in QuickBooks Online.

I'm also adding this reference to ensure records are accurate: Reconcile an account in QuickBooks Online.

If you need further assistance managing your transactions, you can always add comments below. I'll be here to help. Have a good day.

Thanks for the reply.  Customers have paid the invoice through Shopify, but I get an invoice from Shopify that is unpaid and shows as Accounts Receivable.  I'm not sure how to show the invoice paid without generating another deposit somewhere.  It also won't match the deposits I get from Shopify since they are net of fees.  

Thanks for the prompt response and for providing additional information, m-spurgeon. Allow me to chime in on this thread and share some details on resolving this.

Since the invoice was paid in Shopify, I recommend contacting them if they can also provide syncing of the payment transaction of the invoice.

On the other hand, here's how we can manually mark the invoice paid in QuickBooks. Follow the steps below.

To begin, make a receive payment transaction for the invoices:

1. Go to the + New button, then choose Receive payment.
2. Select the Customer in the dropdown.
3. Take note of the amount and the fees of the invoices, as we'll be needing this for the next step.

Then let's now make a bank deposit:

1. Go to the + New button.
2. Under OTHER, choose Bank deposit.
3. Choose the Account.
4. In the Add funds to this deposit section, fill in the necessary details (RECEIVED FROM, ACCOUNT, AMOUNT).
5. Make another line for the fees of the transactions. Input the fees as a negative amount.
6. Click Save and close.

After you've recorded the deposit, match it to the online banking.

Additionally, ensure that you reconcile your accounts to keep them accurate and up to date.

Return to this thread if you need further assistance in managing your invoices in QBO. We'll be here to help you in any way we can. Take care.