Shopify accounting: how to record net payouts and fees correctly

One of the most frequent mistakes we see among Shopify sellers is booking net income (what lands in the bank account) instead of gross income (the total price the customer pays). This makes you lose money in deductions.

How should it be booked?

Correct:

• Income: total sale price (including VAT and shipping).
• Expense: Shopify Payments fee (typically 2.1% + €0.25).
• Expense: payment gateway fee (if you use Stripe or PayPal).

Incorrect: recording only the net amount that reaches your account.

Why does it matter?

If you only record the net, you are losing the deduction of the fees as an expense. In a business with €100,000 in sales, that can mean €2,000-3,000 of undeducted expenses.

At EkonYou we automate the reconciliation of Shopify Payments with your accounts. Contact us.

Do you run an online store? Shopify Partner: VAT registration and filings in more than 50 countries, plus EPR for packaging, electrical equipment and batteries. Shopify accounting →