E-shop integration with accounting: how to save time

Integrating an e-shop with accounting is a solution that small businesses in Lithuania can no longer afford to ignore. Transferring order, invoice and payment data by hand takes time, increases the risk of errors and makes it hard to see the real financial position. Automated order synchronisation with accounting lets data flow from the e-commerce platform straight into the accounting software.

Business transactions are recorded in line with the requirements of the Law on Financial Accounting – without retyping and without delays. In practice, it is convenient to divide an integration into three layers (this is our methodological model, not a legal rule): the commerce platform (orders and customers), the integration layer (API or plugin) and the accounting and tax data layer (invoices, VAT, registers).

In this guide you will learn about integration types, the specifics of the most popular platforms, synchronisation logic, State Tax Inspectorate (VMI) requirements and practical implementation steps – everything a Lithuanian business needs to connect its e-shop to accounting software correctly and securely.

Key takeaways

• Automation is about more than convenience – an e-shop integration with accounting must comply with the Law on Financial Accounting and VAT legislation, not just save time.
• Order status mapping is critical – incorrectly mapped statuses (e.g. “paid” = “delivered”) produce incorrect accounting documents across the whole system.
• VAT configuration needs separate attention – e-commerce integration with VMI reporting works correctly only when VAT codes, transaction types and i.SAF data have been tested in advance.
• Testing before automation is recommended – before switching on daily automatic transfers, it is worth checking at least 10–20 real orders by hand. This is good practice, not a legal requirement.
• Responsibility stays with the taxpayer – even if data is generated automatically, legal responsibility for its accuracy does not pass to the integration or its provider.

What is e-shop and accounting integration, and why do you need it?

E-shop integration with accounting is the automated transfer of data from an e-commerce system (orders, customers, payments, refunds) to accounting software, where accounting documents, registers and tax data are generated.

From a legal point of view, what matters is not the technical connection itself but the result. Business transactions must be supported by accounting documents and recorded so that their content and any corrections can be traced. It is important to meet the requirements for accounting documents.

Automation reduces the risk of manual retyping, but it does not guarantee correct accounting on its own. The company must correctly map product codes, VAT attributes, payment methods, refunds, discounts, delivery charges and order statuses.

Integration is most relevant when:

• Order volume is high – many orders are received every day.
• There are several sales channels – used at the same time.
• Stock and returns need control – up-to-date information is essential.
• Buyers are international – goods are sold to customers in Lithuania and other EU countries.
• Tax reporting is regular – VAT or other data is regularly submitted to the tax administrator.

The most popular e-commerce platforms in Lithuania and their integration options

Several e-commerce platforms are used on the Lithuanian market. Each has its own integration options, but from a tax perspective what matters is not the platform itself but whether the data it transfers allows accounting documents and VAT registers to be generated correctly.

How does WooCommerce accounting work in Lithuania?

WooCommerce accounting is usually implemented through plugins or through the accounting software’s API. It is the most flexible platform because it runs on WordPress and offers a wide choice of integration modules.

From a Lithuanian tax perspective, it matters whether the data transferred from WooCommerce includes: the sale date and document number, the buyer’s identification details, the value of goods, the VAT rate and amount, discounts, delivery and refunds. The specific integration solution depends on the shop version, the payment provider and the accounting system used.

Before implementing an integration, you must check that all the fields required under the VAT reporting rules are transferred.

Does Shopify accounting meet Lithuanian VAT requirements?

Shopify accounting in Lithuania should be assessed by whether all the required accounting and VAT data can be transferred reliably: the sale date, buyer details, value of goods, VAT rate and amount, discounts, delivery, refunds and payment information.

The fact that Shopify issues a document does not prove that it automatically meets all Lithuanian accounting and VAT requirements. The integration must be tested with real Lithuanian VAT scenarios. It is useful to review the structure of the FR0600 return.

Other platforms: PrestaShop, Magento and custom solutions

PrestaShop, Magento and other platforms can be connected in similar ways – through a ready-made connector, an API, a structured file or a custom solution. Technical capabilities depend on the specific platform version and provider – it is advisable to review the provider’s technical documentation before implementation.

How does order synchronisation with accounting work?

Order synchronisation with accounting is a process in which every order created in the e-shop is automatically transferred to the accounting system, where it becomes an accounting document or the basis for one.

What data is transferred automatically?

The integration transfers the following data:

• Order number and date – the key identifiers.
• Buyer details – name/company name, code, VAT number.
• Goods and services – quantities, prices and discounts.
• Delivery charge – a separate line, but it is usually subject to the same VAT treatment as the goods.
• VAT attributes – rate and amount.
• Payment method – the payment method identifier.
• Refunds and adjustments – partial and full refunds.
• Stock changes – inventory updates after each order.

Real-time and periodic synchronisation

Real-time synchronisation transfers data immediately after an order is confirmed. Periodic synchronisation runs at set intervals – hourly or once a day. The choice depends on order volume and the capabilities of the accounting system.

What does a typical integration process look like, from order to document?

1. Cart confirmation – the customer fills the cart and confirms the order.
2. Order creation – the e-shop creates the order with all its data.
3. Payment confirmation – the payment system returns the payment status.
4. Data transfer – the integration sends the order data to the accounting system.
5. Document registration – the accounting system generates or records the accounting document.
6. VAT register entries – the data is assigned to VAT registers and, where applicable, to the i.SAF file.

Mapping order statuses to accounting actions is a key control. “Paid” should not automatically be treated as “delivered”, nor “shipped” as “returned”. Status mapping must follow the rules on revenue recognition and the VAT chargeable event: revenue is recognised on an accrual basis when it is earned (usually when the goods are handed over), not when payment is received, and the VAT liability arises at the chargeable event set out in Article 14 of the Law on VAT (including advance payments).

Under Article 3(3) of the Law on Financial Accounting, business transactions are recorded on the day of the transaction or as soon as possible thereafter, but no later than the date on which the financial statements are prepared (cash transactions – no later than the last day of the current month).

E-commerce integration with VMI: what you need to know

What are the i.SAF requirements for e-shops?

i.SAF is the system for submitting VAT invoice registers, through which taxpayers report sales and purchase VAT invoice data to VMI. Important: there is no direct “integration with VMI” for an e-shop. In this article, “e-commerce integration with VMI” means that the accounting software prepares i.SAF registers and returns from the e-shop data, which the company then submits to VMI.

A few facts about the scope of i.SAF worth knowing:

• Deadline – registers are submitted after the end of the tax period, by the 20th day of the following month.
• Not every order – i.SAF covers VAT invoices, not every B2C order, so not every e-shop order automatically ends up in i.SAF.
• Small business scheme – VAT payers using the small business scheme (SVS) do not submit i.SAF registers.

However, the company must check VAT codes, document numbers, dates, customer identification details and the nature of the transaction. An incorrectly configured VAT code can lead to an incorrect VAT register or VAT return. A testing and reconciliation procedure is essential before starting automatic data transfers.

How do you file VAT correctly using the FR0600 form?

The VAT return form is FR0600. It has separate fields for the taxable amount, purchase and sales VAT, deductible VAT and VAT payable.

The integration must distinguish at least the following VAT scenarios:

• Sale in Lithuania – a standard domestic transaction.
• Sale to a VAT payer in another EU country – an intra-Community transaction.
• Distance sales to consumers in other EU countries – OSS rules. Once the EU-wide distance sales threshold of EUR 10,000 per calendar year is exceeded, VAT is charged at the rate of the buyer’s country.
• Return of goods – a correction document.
• Advance payment – payment received before supply.
• Discount – a price reduction after the sale.
• Delivery charge – usually taxed together with the goods at the same rate; the integration must reflect this.
• Zero-rated or VAT-exempt transaction – these are different regimes with different consequences for VAT deduction.

More information about VAT is available on the VMI VAT page.

How should accounting documents be stored and archived?

Article 10 of the Law on Financial Accounting governs the storage of accounting documents and registers. In practice, an electronic accounting system should ensure the authenticity of documents, the integrity of their content, their availability and the ability to identify who made a change and when.

Legal responsibility for the accuracy of the data submitted remains with the taxpayer, even if the data is generated automatically. It is recommended to keep transfer logs, error messages and correction history.

Article 9 of the Law on Financial Accounting provides for a standard accounting data file (i.SAF-T). It is submitted only at the request of the tax administrator, for example during an audit or investigation. The integration’s data structure should therefore make it possible to generate such a file.

When customers’ personal data is transferred to accounting software or an integrator, a data processing agreement must be concluded with the processor (Article 28 GDPR).

The accounting requirements every company manager must know – including document retention periods and possible fines – are described in detail in our separate article. The current version of the law is available on the Law on Financial Accounting page.

Accounting software with an API: how to choose the right solution?

An API (Application Programming Interface) is a technical interface through which one system automatically passes data to another. Accounting software with an API lets an e-shop send order data directly to the accounting system without manual entry.

It is important to understand that using an API does not in itself confirm that the transferred data will comply with the Law on Financial Accounting or VAT legislation. Data accuracy depends on the configuration.

Accounting software with API capabilities known in Lithuania includes, for example, Rivilė and Directo. However, the specific API features of each program must be checked against the provider’s current technical documentation.

What should you consider when choosing accounting software for integration?

• Completeness of data transfer – whether products, customers, orders, refunds and payments can be transferred.
• VAT scenarios – whether VAT codes and multiple VAT scenarios are supported.
• Error handling – whether there is an error log and retransmission.
• Change history – whether the history of changes is kept.
• Access rights – whether access rights can be controlled.
• Return exports – whether the system can export data for i.SAF and other returns.
• Support for legislative changes – whether the provider keeps the software up to date when legislation changes.

What is the difference between a ready-made plugin and a custom integration?

A ready-made plugin is quick and simple, but often has limited VAT configuration and does not always cover all Lithuanian tax scenarios. A custom integration matches the business process more closely, but requires more testing, maintenance and responsibility.

In more complex cases – high turnover, varied VAT scenarios or several sales channels – professional accounting services for business, including tax oversight of integrations, can help assess these solutions. In both cases, e-commerce integration with VMI reporting requires proper VAT configuration.

More on tax administration – on the VMI tax administration page.

Practical steps: how to connect an e-shop to accounting software

Why is it important to describe the process in advance?

Before connecting the systems, you need to define when an order is created, when it is considered paid, when the document is issued, how a refund is recorded and when stock is reduced. Without a clear process description, the integration will not work correctly.

What access do you need to collect before implementation?

You will need: e-shop administrator access, payment provider details, the accounting system API key, the VAT configuration and the product and customer reference lists. Access should be granted on a least-privilege basis – the integrity of accounting data is an important element of how accounting is organised.

How do you map reference lists and codes correctly?

You need to map product codes, customer identifiers, the chart of accounts, VAT codes, payment methods and warehouses. Mismatched codes are one of the most common reasons why automatic transfers create incorrect accounting entries.

If accounting has not been kept for a long time or the data is disorganised, you may need a neglected accounting clean-up service before implementing an integration.

How do you test and reconcile the integration results?

It is recommended that test scenarios cover at least:

• Successfully paid order – the main scenario.
• Unpaid or cancelled order – status mismatch.
• Partial refund – checking the correction document.
• Full order refund – the full credit note scenario.
• Discount – price adjustment.
• Delivery charge – a separate line on the document.
• Sale with VAT payer details – a B2B transaction.
• Sale to a foreign customer – a cross-border scenario.
• Repeated or duplicated notification – duplicate handling.

Return scenarios are directly shaped by consumer rights: a consumer usually has a 14-day right to withdraw from a distance contract, so the integration must reliably handle refunds even after the order has been fulfilled.

After testing, compare the e-shop turnover, the payment provider report, revenue in the accounting system, VAT amounts, refunds and bank receipts. The fact that the integration returned no technical error does not mean the accounting result is correct.

The requirements for recording transactions can be found in the current version of the Law on Financial Accounting.

Key tax elements when integrating an e-shop

Main tax obligations when integrating an e-shop with accounting in Lithuania

Tax or obligation	Return or form	Note
VAT return	FR0600	Separate fields for the taxable amount, purchase and sales VAT, deductible VAT and VAT payable
VAT invoice registers	i.SAF	Prepared automatically through the integration, but VAT codes and the nature of transactions must be checked
Corporate income tax	PLN204	Annual corporate income tax return – relevant for a private limited company (UAB) running an e-shop
Personal income tax return	GPM311	Annual individual return – relevant for a self-employed online seller

* Specific rates, thresholds and deadlines may change, so it is advisable to check the current version on the VMI website before filing returns.

Summary and recommendations

E-shop integration with accounting should be seen as an accounting control process, not just a convenient way to move data. E-commerce integration with VMI reporting requires ongoing attention to VAT configuration and data accuracy.

For a business that still retypes everything by hand, a sensible starting point is:

1. Process description – describe the order and refund flow.
2. Field definition – identify what data an accounting document needs.
3. Code mapping – map VAT and accounting codes between the systems.
4. Trial transfer – run a controlled test transfer of data.
5. Data reconciliation – compare e-shop, payment and accounting data.
6. Switching on automation – only then launch daily automatic transfers.

A professional integration is most justified when orders grow, several channels appear, VAT scenarios become more complex or refund and stock errors become frequent. If you are not sure whether your current accounting meets all legal requirements, we recommend reading our article on accounting obligations and fines – it explains who must keep accounts and what penalties apply for breaches.

Need help integrating your e-shop with accounting?

If you want your integration to work correctly from day one, contact accounting specialists who understand both the technical and the tax details. Our team will help assess your e-shop’s situation, choose the right integration method and make sure your VAT configuration complies with Lithuanian law.

Contact our accountants today – the first consultation is free.

Frequently asked questions