Connecting an e-shop to accounting step by step

The short answer

You connect an e-shop to accounting by having orders, invoices and payments transferred automatically via API or XML import into your invoicing or accounting software, for example SuperFaktúra, Pohoda, Money S3 or SaveÚčto in Slovakia, or Fakturoid and iDoklad in the Czech Republic. The process has five steps: decide where the invoice is created, map the data, choose the integration method, handle exceptions and test on real orders; a simple integration takes us, indicatively, about one day.

This article is about invoicing and accounting. If you need to sync stock, production and orders with an ERP, see the article How to connect an e-shop with an ERP system.

Step 1: Decide where the invoice is created

This is the most important decision and the most common source of chaos. There are two options:

• The e-shop issues the invoice and the finished document is transferred to accounting. Advantage: the customer receives the invoice together with the order confirmation.
• The invoicing software issues the invoice based on data from the e-shop. Advantage: one document numbering sequence and one place where your accountant finds everything.

Never both at once. Two systems issuing invoices with their own numbering sequences are a guaranteed problem in checks and audits.

Step 2: Map the data to transfer

• customer: name or company, company ID, tax and VAT IDs, billing and delivery addresses,
• line items: name, quantity, price, VAT rate, discounts,
• shipping and payment fees as separate lines with the correct VAT,
• payment method, variable symbol (payment reference), currency,
• payments from the payment gateway or bank,
• returns and credit notes.

Step 3: Choose the integration method

Each program offers different options. An indicative overview:

Software	Typical integration method	Note
SuperFaktúra	REST API	suitable for issuing an invoice straight from the order
Pohoda	XML import and export, mServer	often runs locally at the accountant's, so you must decide where the import happens
Money S3	XML data exchange	correct setup of numbering sequences and warehouses is key
SaveÚčto	public API	our own invoicing and accounting system for sole traders and small companies
Fakturoid, iDoklad	REST API	common choices in the Czech Republic

Ready-made platforms also have plug-ins for these connections. They are worth trying, but check that they cover credit notes, foreign customers and your VAT rates. If not, a custom integration tends to be more reliable.

Step 4: Handle the exceptions

A standard order is connected quickly. Exceptions are what cost time and nerves:

• Duplicate invoices. If a transfer is repeated (outage, resend), no second invoice may be created. Every order needs a unique identifier.
• VAT rounding. The e-shop and the accounting software may calculate VAT per line or on the total. A difference of a few cents on an invoice is exactly what your accountant does not want to chase.
• Discounts and coupons. A discount must carry the correct VAT rate, not be a single negative line without one.
• Returns and credit notes. Returned goods should create a corrective document, not delete the original invoice.
• Foreign customers. Another currency, OSS for sales to consumers in the EU, reverse charge for VAT-registered businesses.
• The other side being down. If the accounting software is unavailable, data should be queued and synced later, with an alert if it keeps failing.

Step 5: Test on real orders

One test order is not enough. We recommend going through at least these cases: a VAT-registered company, a private person, an order with a discount, cash on delivery, card payment, a return and a foreign customer. Have your accountant check the result, not just the developer. They know best what the documents should look like.

When an export is enough and when you need an API

Not every e-shop needs a real-time integration. With a few orders a day it may be enough for the e-shop to generate an XML file once a day for the accountant to import. It is cheap and simple, but someone has to remember it, and errors only show up during the import.

An API connection sends the document right at the order or payment, reports errors immediately and needs no manual step. It pays off when you have more orders, want to send invoices to customers automatically or need to know about payments right away. The decision does not have to be final: starting with an export and moving to an API later is a common path.

What to prepare before we start

• access to the e-shop admin and to the invoicing or accounting software (a test account, if there is one),
• an API key, or where Pohoda or Money S3 runs and who has access to it,
• document numbering sequences and the rules your accountant uses,
• a list of VAT rates, shipping and payment methods,
• a few real orders that caused problems.

Matching payments

The invoice is half the job. The other half is knowing whether it has been paid. Payment gateways can send payment confirmations directly; bank transfers are matched by the variable symbol from the bank statement. When this works, the e-shop can ship goods automatically after payment and your accountant does not have to tick off payments by hand.

After launch: maintenance and changes

An integration is not finished once and for all. Invoicing programs change their APIs, the state changes VAT rates, the e-shop adds a new shipping method. A good integration therefore sends an alert when a document fails to transfer and keeps a log showing what happened to each order. Smaller changes, such as a new rate or payment method, can then be handled as an express change, often within an hour.

Cost and timeline

A simple integration (orders and invoices in one direction into one program) takes us, indicatively, about one day. Payments, credit notes, multiple currencies or stock add more work. We charge €38 per hour excl. VAT and you get an estimate of hours before we start. More on the Integrations and API page, or for a custom e-shop see Websites and e-shops.

We will connect your e-shop to accounting

Tell us which platform your e-shop runs on and which software your accountant uses. A senior will propose an approach and estimate the time. Get in touch.