The most common mistake is recording the deposit that hits your bank account as sales revenue. That deposit is net of Shopify’s fees, so you’re understating your actual revenue and not tracking what you’re paying in fees. Both problems matter for understanding your business.

Record gross sales as revenue. If a customer pays $100 for a product, that’s $100 in sales regardless of what Shopify keeps. Your top line should reflect what customers actually paid, not what landed in your bank account after fees.

Track Shopify fees as a separate expense account. Payment processing fees, Shopify Payments transaction fees, and subscription fees should all be visible on your profit and loss statement. These costs add up quickly and you need to see them to manage them. Most Shopify sellers are paying 2.5% to 3% on every transaction, which on $500,000 in annual sales is $12,500 to $15,000 in fees alone.

The timing creates a reconciliation challenge. Sales happen throughout the day, but Shopify batches payouts and sends them every few days. A payout hitting your bank on Tuesday might include sales from Friday, Saturday, Sunday, and Monday. This means your daily sales in Shopify won’t match your daily bank deposits.

Use a clearing account to bridge the gap. Create an account called something like “Shopify Clearing” or “Shopify Deposits in Transit.” When you record sales, the offset goes to this clearing account instead of directly to your bank. When the payout arrives, you clear it from that account to your bank account. The clearing account balance at any point represents money Shopify owes you that hasn’t been deposited yet.

Here’s the flow in practice. A customer buys a $100 item. You record $100 in sales revenue with the offset going to your Shopify clearing account. Shopify takes $2.90 in fees. You record $2.90 as a payment processing expense, reducing the clearing account. When the $97.10 payout hits your bank, you move that amount from clearing to your checking account. The clearing account nets to zero for that transaction.

You can do this manually or use integration tools. Apps like A2X, Synder, or the native Shopify connection in QuickBooks can automate the breakdown of gross sales, fees, and other adjustments. Manual entry works fine for lower volume stores, but if you’re processing hundreds of orders monthly, automation saves significant time and reduces errors.

Don’t forget about refunds and chargebacks. These need to be recorded as reductions to revenue, not as expenses. Shopify will reduce your payout when refunds happen, so your clearing account reconciliation needs to account for these adjustments.

Reconcile your Shopify payouts to your bank at least weekly. Download the payout report from Shopify, compare it to what hit your bank, and make sure your clearing account balance makes sense. Discrepancies caught early are easy to fix. Discrepancies caught at year end during tax prep are painful.

If your e-commerce bookkeeping has been recording net deposits as income, you’ll need to go back and restate things correctly. Your total profit stays the same, but your revenue will increase and you’ll have a new expense line for fees. This gives you a more accurate picture of your business and proper documentation if you ever need to show financials to a lender or buyer.

Getting this right from the start saves hours of cleanup later. If your books are already a mess from months of recording payouts incorrectly, a good small business bookkeeper can untangle it and set up a system that works going forward.