reconcile synced Shopify sales and fees with deposits

Hello Anca1, 

Welcome to the Community page, 

You can match the deposit and resolve the difference at the bottom so you can allocate the transaction fee,  that's if the sale is recorded with the fee taken out already in your QuickBooks Online account. 

@Anca1 

Another option, you can use a 3rd party connector app to reconcile Shopify transactions and avoid duplication.

we use the Shopify connector by QuickBooks and it syncs the full value of sales and the transaction fees to an expense account. If I match the deposits by adding transaction fee at the bottom do I have to delete the transactions in the expense account to prevent doubling?

Thanks for getting back on this thread and adding some additional information about your concern, @Anca1.

I'm here to help you manage your transactions in QuickBooks Online.

Since the full values of the sales and the transaction fees were already synced into QBO using a connector, it can cause duplicate if you match those deposits by adding those fees.

To prevent duplicates, yes, you can delete the transactions from the expense account. For the best approach to handling this kind of situation, you can reach out to your accountant to ensure the accuracy of your books.

Check out this article for detailed information on the integration process: Shopify and QuickBooks Online Integration Guide.

Also, I’m sharing these articles for your guide when reconciling your transactions:

• Learn the reconcile workflow in QuickBooks
• Reconcile An Account In QuickBooks Online

You can always count on us if you have other banking-related queries. We're always here to help.