Shopify accounting reconciled to the cent
Sales, fees, payment gateways, VAT in each country, imports and refunds, properly booked and without copying orders by hand.
In short
We keep the accounts and taxes of your Shopify store: sales at their gross amount, fees as expenses, Shopify Payments, PayPal and Stripe payouts reconciled with the bank, VAT for each country through OSS, IOSS or a local number, and refunds with their credit note.
Shopify sales flow into the accounts automatically, without copying them by hand, and every close reconciles to the cent with what is declared in each country.
What's included
Sales and invoices
Properly configured invoice series, an invoice for every order, credit notes for every refund and a system ready for Verifactu.
Payment gateways
Shopify Payments, PayPal, Stripe, Klarna and others: gross sale, fee as expense and payout reconciled with the bank.
International VAT
The €10,000 threshold, OSS and IOSS and local VAT numbers, each in its own account.
Imports
EORI, import VAT, duties and customs declarations booked properly, with the VAT recovered on Form 303.
Legal form
Sole trader or limited company: when it pays to switch and how to do it. Plus Spanish registration for foreign companies.
Automation
Shopify sales flow into the accounts on their own and every period is checked against the store, the bank and each country's returns.
The mistakes we see most in Shopify stores
| Mistake | What it causes | How to do it right |
|---|---|---|
| Booking what reaches the bank | Undeducted fees and VAT that doesn't reconcile | Gross sale to income and fee to expense |
| Still charging Spanish VAT after passing €10,000 | Wrongly charged VAT and surcharges | OSS registration and the customer's country VAT |
| Refunding without a credit note | Inflated sales and VAT | A credit note for every refund |
| Holding stock in another country without registering there | Undeclared sales in that country | A VAT number there before moving the goods |
| Importing small consignments without IOSS | The customer pays VAT and fees on delivery, and returns the parcel | IOSS and VAT charged at checkout |
| Shipping to Germany or France without a packaging registration | Marketplace blocks and penalties | EPR in each country |
| Booking US sales tax as income | Inflated profit and unpaid tax | A liability to each state and a state return |
Dig deeper on our blog: Shopify net payouts and fees · refunds and credit notes · IOSS and customs · dropshipping and VAT · multi-currency Stripe and PayPal.
Frequently asked questions
How are Shopify Payments payouts booked?
At the gross amount of each sale, not at what reaches the bank. The sale goes to income for the total the customer pays and the Shopify fee is recorded separately as an expense. If you only book the net, you lose the deduction of the fees and the sales don't reconcile with the VAT declared.
How is a Shopify refund handled for accounting purposes?
With a credit note that cancels the original invoice in full or in part. A refund in Shopify without its credit note throws sales and VAT out of balance.
Do I have to invoice every Shopify order?
Yes. Every sale needs its invoice or simplified invoice, with consecutive numbering. Shopify can generate them, but the series and tax details have to be set up correctly from the start, and from 2027 the invoicing system must comply with Verifactu.
How do I book sales in several countries with different VAT?
Each country and each rate in its own account, with OSS VAT kept separate from the local VAT of the countries where you hold stock. The automation splits it from the Shopify reports.
And sales in the United States or in other currencies?
They are booked in euros at the exchange rate of each transaction, with Stripe or PayPal exchange differences recorded separately, and the sales tax collected as a liability to each state, not as income.
Do you also keep the accounts of my company if it is foreign and sells in Spain?
Yes. For companies from outside Spain: Spanish VAT, the fiscal representative if needed and, if you have an establishment here, full accounting.
Tell us about your store
Book a 15-minute call or write to us. We'll tell you what you need: VAT registration in whichever country, OSS and IOSS, EPR, US sales tax or your store's accounting. No obligation.