Accounting on Shopify

1. 8. 2026
Účetnictví na Shopify

Connecting accounting and invoicing to Shopify saves Czech e-shops hours of manual work – it automatically issues an invoice for every order, keeps track of payments and passes the data on to your accounting system. On Shopify, the most common setups are Fakturoid (online invoicing) and the POHODA accounting system, with no retyping of orders between systems.

In this guide, we'll go through why you should automate accounting on Shopify, how the Fakturoid and POHODA integrations work, what an integration gives you and what to watch out for with VAT and invoice numbering sequences.

Key takeaways

  • Fakturoid connects to Shopify through an app and an open API – invoices are created automatically for orders.
  • The integration can match payments, track whether invoices have been paid and email invoices to customers.
  • POHODA connects via XML / mServer or middleware – transferring orders, invoices and stock.
  • Automation saves time and reduces errors in your accounting.
  • Keep an eye on correct VAT rates, numbering sequences and currencies.

Table of contents

Why connect accounting to Shopify

Without an integration, every order means manually issuing an invoice, checking the payment and retyping it into your accounting – repetitive work that takes hours a week as volume grows and leads to mistakes. Automation solves this: the invoice is created on its own, the payment is matched and the data flows into your accounting system. Instead of doing admin, you can focus on selling and be confident that your documents add up. Connecting your accounting is therefore not just a technical gadget, but one of the decisions that takes the most day-to-day routine off a growing e-shop.

Automation also pays off at year-end closing and during audits. When documents are created consistently and continuously matched with payments, your books are in order all year round and you don't have to chase anything retroactively. The more orders you process each day, the more manual invoicing becomes a bottleneck – and the sooner the integration pays for itself.

Fakturoid on Shopify

Fakturoid is a popular Czech online invoicing service, and it connects to Shopify through an app built on its open API. After installing the app, you link it to your Fakturoid account, choose a bank account and set when invoices should be created – right after the order is placed, or only once it has been paid.

The integration then automatically creates invoices for orders, matches them with payments, tracks whether they have been paid and can email them to customers. The result is invoicing that runs by itself in the background.

Thanks to its cloud-based nature, Fakturoid is usually the fastest way to automate invoicing on Shopify. It suits e-shops that want their documents in order without investing in complex infrastructure, and it can also send payment requests and reminders. For most small and medium-sized Czech e-shops, it's a practical starting point.

POHODA on Shopify

POHODA by Stormware is one of the most widely used Czech accounting and inventory systems, used by many companies across industries. Connecting it to Shopify is usually done via the XML interface / mServer or through middleware that transfers data between the two systems. You can transfer orders, invoices, stock levels and customers, so your accounting and inventory stay in sync with your e-shop.

Because POHODA typically runs locally or on a server, the integration is technically more demanding than with the cloud-based Fakturoid – so it's a good idea to leave setting up the connection and data mapping to an experienced developer.

What the integration makes possible

Automatic invoices. A document is created for every order without manual intervention.

Payment matching. The system links the payment to the order and marks it as paid.

Sending documents. Invoices are emailed to customers automatically.

Inventory sync. With POHODA, stock and availability can be kept in sync with your e-shop.

Overview for your accountant. The data is ready in the accounting system, with no manual retyping.

Fakturoid or POHODA: which one is for you

Fakturoid is ideal for small and medium-sized e-shops that want simple cloud invoicing with a quick integration. POHODA suits companies that already keep their accounting and inventory in POHODA and need to connect the e-shop to their existing processes. Many companies combine both – depending on where they keep their books and how complex their inventory management is.

When deciding, consider who will be working with the documents. If your accounting is handled by an external accountant via Fakturoid, the choice is clear. If you have your own accounting department used to POHODA and a large warehouse, it's worth investing in a more robust integration. Either way, the goal is the same: no manual retyping and documents that add up.

Step by step: connecting Fakturoid to Shopify

  1. Install the app. Add the Fakturoid integration app to Shopify and confirm the installation.
  2. Link your account. Connect the app to your Fakturoid account, granting it access.
  3. Choose a bank account and paste in the webhook URL from Fakturoid.
  4. Set when to invoice – right after the order, or only after payment.
  5. Set up numbering sequences, VAT rates and currencies so your documents are correct.
  6. Place a test order to verify that the invoice is created, matched with the payment and sent by email.

Once set up, invoicing runs automatically – a document is created for every order without manual intervention.

Fakturoid vs POHODA: comparison

Criterion Fakturoid POHODA
Type Online (cloud) Desktop / server
Shopify integration App + API XML / mServer / middleware
Implementation effort Low Higher (developer recommended)
Inventory Limited Full inventory management
Best for Small and medium-sized e-shops Companies with their own accounting department and warehouse

In short: if you want a quick and simple invoicing solution, go for Fakturoid. If you already keep your accounting and inventory in POHODA and need to connect the e-shop to your existing processes, a more robust POHODA integration makes sense.

What happened to EET

You may still come across mentions of EET (Czech electronic sales records) in connection with invoicing. For the record: EET has been abolished in the Czech Republic and you no longer need to record sales through this system. So if you see a guide on connecting EET somewhere, it's no longer relevant today. Your obligations remain issuing documents correctly and paying VAT – and that's exactly what a Fakturoid or POHODA integration takes care of.

VAT, OSS and numbering sequences in practice

When it comes to e-shop accounting, there are three things worth getting right from the start. The first is correct VAT rates on products – the standard and reduced rates must be right, otherwise you'll pay the wrong amount of tax. The second is the OSS scheme for selling to consumers in the EU, which lets you pay VAT according to the destination country through a single return; your invoicing integration must pick up these rates correctly. The third is numbering sequences – consistent invoice numbering without duplicates, especially when documents are created automatically.

These things are interconnected, and it's best to set them up together so that documents are correct across both your e-shop and your accounting.

How much time automation saves

The benefit of connecting your accounting is best seen in everyday operations. Without automation, every order means manually issuing an invoice, checking the payment in your bank account and matching it, and possibly sending the document to the customer. With ten orders a day it's annoying; with fifty or more, it becomes a full-time job – and it's not an activity that generates any revenue for the e-shop.

With Fakturoid or POHODA connected, these steps disappear. The invoice is created automatically, the payment is matched and the document is sent on its own. Instead of retyping data, your accountant only checks and closes the books, which saves time as well as the cost of external processing. The more orders you process, the sooner the integration pays for itself – and that's not counting the value of having your documents in order all year round.

How automation reduces errors

Manual retyping is the most common source of errors in e-shop accounting – a typo in an amount, the wrong VAT rate, a forgotten invoice or a duplicate document number. Every such mistake means extra work tracking it down and fixing it, and in the worst case a problem during a tax audit.

An automatic integration significantly reduces these errors, because data flows between Shopify and your accounting without human intervention and according to rules set up once. Documents have consistent numbering sequences, correct rates and linked payments. The result is not just time saved but, above all, peace of mind – you know your accounts add up and you don't have to chase anything manually at the end of the month.

What to watch out for

  • VAT rates. Check that the rates are correct and properly reflected in your documents, especially when selling to the EU (OSS scheme).
  • Numbering sequences. Set up consistent invoice numbering to avoid duplicates.
  • Currencies. When selling in foreign currencies, watch exchange rates and rounding.
  • Time of issue. Decide whether to invoice after the order is placed or only after it has been paid.

When to set up the accounting integration

Ideally, you should think about connecting your accounting as early as when building or migrating your e-shop – VAT rates, numbering sequences and invoicing then fit into the whole from the start and you don't have to redo anything. If your e-shop is already running and you handle invoicing manually, a good signal to connect it is the moment when document admin starts eating into time you'd rather spend on selling.

Definitely don't wait until manual invoicing becomes a daily burden or a source of errors. The integration can be deployed while the store is live, without interrupting sales – with Fakturoid it's a quick solution, while with POHODA you need to count on a more demanding setup. In both cases, the sooner you introduce automation, the more time and stress you'll save and the sooner your books will be in order.

Whichever solution you choose, we recommend having the integration set up and tested in one go, ideally together with your e-shop's other integrations. Accounting is tied to payments, shipping and VAT – and when all the parts work together, your e-shop runs smoothly without unnecessary manual work.

What automated invoicing looks like in practice

Imagine an ordinary day at an e-shop with connected invoicing. A customer completes an order and pays. At that moment, an invoice is automatically created in the background with the correct VAT rate and a number from the prepared numbering sequence. As soon as the payment arrives in your account, the system matches it with the order and marks it as paid. The document is emailed to the customer without you lifting a finger.

You or your accountant then just check everything instead of retyping, and close the books at the end of the period. When a return comes in, a corrective document is issued according to the same rules. The whole cycle runs reliably and without manual intervention, so you can focus on selling and looking after your customers. That's exactly the value of connecting your accounting – not a single invoice saved, but an entire process that takes care of itself and doesn't make mistakes.

Accounting as part of the whole e-shop

Invoicing doesn't stand alone in an e-shop – it's tied to payments, shipping and taxes. The invoice has to match how the customer paid, which shipping method they chose and which VAT rate applies to the product. That's why it pays to see accounting as one part of a bigger whole, not as an isolated integration.

When all the parts work together, the e-shop runs smoothly: an order is paid, shipped, invoiced and booked without you having to step in. It's precisely connecting accounting with the other integrations (payments, carriers, VAT and OSS) that turns an e-shop into a system that largely runs itself. As a Shopify agency, this kind of interconnected setup is exactly what we focus on – so that the individual parts don't form isolated islands but work together.

Frequently asked questions (FAQ)

Can Fakturoid be connected to Shopify?

Yes. Fakturoid connects through an app built on its API. Invoices are then created automatically for orders, payments are matched and documents are sent by email.

Can Shopify be connected to POHODA?

Yes, usually via XML / mServer or middleware. You can transfer orders, invoices, stock and customers. The integration is technically more demanding and is best left to a developer.

Is the invoice issued automatically?

Yes. You set whether the document is created right after the order or only after payment, and the integration issues it without manual intervention.

Can the integration handle EU sales and VAT?

Yes, but you need to set up VAT rates correctly and, if applicable, the OSS scheme for selling to the EU. We take care of this when setting up the integration.

Do I have to pay for the integration separately?

With third-party apps, usually yes – the integration is a separate product on top of Fakturoid or POHODA itself. The specific pricing model depends on the solution you choose.

Do I still have to deal with EET?

No. EET has been abolished in the Czech Republic, so you no longer record sales through this system. You only need to issue documents correctly and pay VAT.

How long does it take to connect Fakturoid?

For a standard e-shop, it's a quick deployment – installing the app, linking the account and configuring it. A POHODA integration is more demanding and is best left to a developer.

Does the integration also issue corrective documents and credit notes?

Yes, depending on the chosen solution and its settings. It's a good idea to think through returns and corrective documents when setting up the integration, so that cancellations and credit notes are also created consistently and your accounts add up.

Can the integration handle invoices in foreign currencies?

Yes, but you need to set up currencies, exchange rates and rounding correctly. We take care of this when setting up the integration.

Want automated invoicing on Shopify?

We'll connect Fakturoid or POHODA to your Shopify store so that invoices are created on their own and your accounts add up. Take a look at our Shopify e-shop development and integrations or book a free consultation.

Sources

Author: Miroslav Volovec, CEO of 3NODE Software s.r.o. — specialists in developing and integrating e-shops on the Shopify platform.