The deposit from Shopify is not your sales number. Shopify deducts payment processing fees, transaction fees, and any refunds before sending you money. If you record the bank deposit as sales income, your revenue will be understated and those fees will be invisible in your books.

The correct approach is recording gross sales separately from the payout. Your total sales go to an income account. Processing fees go to an expense account. Refunds reduce your sales. The net amount after all that should match what actually lands in your bank account.

In QuickBooks, set up a clearing account for Shopify. This can be an Other Current Asset account or a bank-type account. When you record sales, the money goes into this clearing account rather than directly to your checking account. When you record fees and refunds, they reduce the clearing account balance. When Shopify deposits money into your actual bank account, you transfer that amount from the clearing account to checking. If everything is recorded correctly, the clearing account zeros out after each payout.

For manual recording, pull Shopify’s payout reports and enter summary amounts for each deposit. Create a sales receipt or journal entry showing gross sales, fees, and refunds. Match this to the bank deposit. This method works for low-volume sellers but becomes tedious quickly if you’re processing dozens of orders daily.

Integration apps handle this automatically. A2X is the most reliable option for Shopify-to-QuickBooks connections. It pulls your payout data, breaks it into correct categories, and posts accurate journal entries. The cost is usually worth it for anyone doing real volume. Other options include the native Shopify connector and apps like Webgility, though A2X tends to handle the accounting more precisely.

Sales tax adds complexity. Shopify collects tax from customers, but that money isn’t your income. It’s a liability you owe to the state. Your books need to track tax collected separately and show it flowing through to your sales tax payments. Integration apps typically handle this categorization automatically.

Reconcile your Shopify clearing account monthly. If the balance isn’t close to zero, something is off. A payout wasn’t recorded, fees were missed, or sales got duplicated somewhere. Catching these issues monthly is much easier than untangling a year of e-commerce transactions at tax time.

If you’re running a Shopify store and struggling to make sense of the numbers, a Richmond bookkeeper familiar with e-commerce can set up your accounts correctly from the start. Getting the structure right means your reports actually show true sales and real profit margins instead of numbers that don’t quite add up.