Shopify or WooCommerce generate hundreds of orders, yet your accounting cannot see them — it only sees bank movements and payment-gateway statements. Without proper integration, sales, payments and invoices drift apart and nothing reconciles at month end. The goal is simple: every order should have its payment and its document, and VAT should land on the day it actually arose.
Why connect Shopify and WooCommerce to your accounting at all?
An e-commerce platform and your accounting speak two different languages. Shopify records orders and statuses, the payment gateway (Stripe, GoPay, PayPal) records payouts to your account after deducting its fee, and your accounting software records invoices and revenue. If you do not link these three flows, revenue will not match what actually reached your bank.
Good integration means each order has a matched payment from the gateway statement and a document issued to it. Only then can you reliably say how much you earned, how much the gateway took, and how much VAT you owe. For the basics of getting bookkeeping right, see our guide to professional accounting in Slovakia.
How do you match orders, payments and invoices?
The basic rule is: one order — one payment — one document. In practice this means linking the payment-gateway statement so that each incoming amount is matched to a specific order and invoice. The gateway fee the platform withholds is posted separately as an operating cost — you report revenue in full and the fee apart, not the “net” amount.
With a high order volume, revenue is commonly posted in summary — a daily or monthly close from the gateway — rather than order by order. The condition is that the summary ties back to individual documents and stays provable under the Accounting Act. Example: a shop with 800 orders a month posts one monthly sales recap with the gateway report attached.
Does an e-shop need a cash register (eKasa)?
This is the most common worry, and the answer pleases most owners. If the shop takes payments exclusively cashlessly — bank transfer, card online via a payment gateway — there is no obligation to record sales through the Slovak eKasa cash-register system. The money arrives directly to the account, away from any point of sale, and is not cash received by the seller.
Cash on delivery paid to the post office or courier does not trigger eKasa either — the cash is taken by the carrier, not by you. You would only need a cash register if you received cash directly, for example at in-person pickup paid in cash. From 1 January 2026 a new act on sales records (No. 384/2025 Coll.) applies, but nothing changes for a cashless shop or cash on delivery.
When does VAT become due on an online payment?
In e-commerce the customer usually pays first and the goods ship later — and that determines the VAT moment. Under Section 19 of the Slovak VAT Act, the tax point is the day of supply, but if payment is received before the supply, the liability arises on the day the payment is received, up to the amount received.
For a VAT payer this means the decisive date is when the money arrives through the gateway, not the dispatch date. Example: the customer pays by card on 28 March and you ship on 2 April — the VAT belongs to March. That is why the integration must know the payment date from the gateway statement, or VAT ends up in the wrong period.
What about selling abroad and the OSS scheme?
If you sell goods to end consumers in other EU countries, watch the annual threshold of EUR 10,000 across all such supplies combined. Below it you apply Slovak VAT; above it the place of supply moves to the customer’s country and you must apply the VAT rate of the country of consumption.
From there you either register for VAT in each destination country or use the OSS scheme and remit the foreign VAT in a single return. The integration must therefore be able to tell the customer’s country and assign the correct rate — otherwise the OSS return cannot be compiled reliably. Where cross-border VAT gets complicated, it pays to lean on Slovak tax advisory for companies.
How do you avoid the most common integration mistakes?
The first mistake is posting the “net” gateway amount and losing both the fee and the true revenue figure. The second is assigning VAT by dispatch date instead of payment date. The third concerns foreign currency: selling in another currency creates exchange-rate differences that must be converted at the reference rate and posted to income or expense.
The fix is an automated link that pulls orders, payments and rates into one place, plus a regular monthly reconciliation of the gateway statement against the books. Once these three flows are set up correctly, the close stops being detective work and the numbers reconcile on their own.
Running Shopify or WooCommerce and your sales do not match the books? We connect the payment gateway, sales and invoices so every order has its payment and document, and VAT lands in the right period.
FAQ
Does a Slovak e-shop need a cash register?
If you take payments only cashlessly (transfer, card online, payment gateway), there is no eKasa obligation. Cash on delivery paid to a courier or the post office does not trigger it either, because the carrier takes the cash. You would need a register only when receiving cash directly, such as in-person pickup paid in cash.
When do I account for VAT if the customer pays in advance by card?
On the day the payment is received. Under Section 19 of the Slovak VAT Act, when payment is received before the goods are supplied, the liability arises from the amount received on the day it arrives, not at dispatch. The gateway credit date is decisive.
How do I post payment-gateway fees?
Separately, as an operating cost. You report revenue in full and post the fee the gateway withholds apart, in expenses. Posting only the “net” amount after the fee is a mistake that distorts both revenue and the VAT base.