Quick answer
For a small company, choosing accounting software in Estonia usually comes down to four local online programs. Merit Aktiva is the best known. SimplBooks and SmartAccounts have cheaper entry plans that suit founders who keep their own books, while the state-run e-Financials is free for the first year. All four have an English interface and prepare Estonian tax returns, unlike foreign software such as Xero. If an accountant keeps your books, the simplest choice is usually the program they already work in.
Every Estonian company has to keep accounts, even one with no employees and a few sales a year. The books feed the VAT return once the company is registered for VAT, the payroll tax return when it pays salaries, board fees or dividends, and the annual report that every OÜ files through the e-Business Register.
Founders from abroad, e-residents included, often start with a tool they already know, such as Xero or QuickBooks, and find out later that it cannot produce Estonian returns. This guide compares the main accounting software in Estonia on the points that matter for a small company run from abroad, and shows when it is simpler to leave the books to an accountant.
What Accounting Software in Estonia Has to Do
The legal requirements are the same whichever program you choose, so the difference is how much routine work the software takes off your hands. Five things matter most:
- Tax returns. Good software prepares the monthly VAT return and payroll tax return, then either sends them to the Estonian Tax and Customs Board or produces a file you upload. A direct connection is about to matter more: the payroll tax return is already submitted as data straight from the software, and from April 2027 the VAT return follows, although manual entry and file upload will remain possible. Our Estonian company tax calendar lists the deadlines.
- The annual report. The balance sheet and income statement should come out of the program in a form the e-Business Register accepts. The notes, and for all but the smallest companies the management report, still have to be written by someone.
- Bank connections. A direct connection imports bank statements and matches payments to invoices. It usually covers only the main Estonian banks, so for Wise, Revolut and similar accounts you upload statement files.
- E-invoices. Estonian buyers can ask for electronic invoices, so the program should send and receive them.
- Language. The interface should be available in English, not only in Estonian.
Merit Aktiva vs SimplBooks vs SmartAccounts vs e-Financials
The table compares the entry-level plans that suit a small company, with prices per month and excluding VAT unless stated otherwise. An entry is one booked transaction, such as an invoice or a payment.
| Feature | Merit Aktiva | SimplBooks | SmartAccounts | e-Financials |
|---|---|---|---|---|
| Price | Standard €19, Pro €39 | MINI €9.90 (invoicing only), Start €16.90, Premium €29.90 | Starter: prepaid entries, 25 for €9; Pro €27 | After the first year, €5 a year or €5 to €9 a month by number of entries |
| Free period | Free version for the first 6 months, limited to 100 sales invoices, 100 purchase invoices and 100 entries | 30-day trial | 30-day trial | First year free |
| Interface | Estonian, English, Russian | Estonian, English, Russian | Estonian, English | Estonian, English |
| Direct bank connections | LHV, SEB, Swedbank, Coop | LHV, SEB, Swedbank, Coop | Pro plan only; Starter imports statement files | Statement files uploaded manually |
| Tax returns | Prepared and sent from the program | VAT return and payroll tax return sent directly | Sent directly on Pro; as an XML file on Starter | Prepared and submitted from the program |
| Annual report | Report file to upload to the register; micro companies can also send it directly | Built-in annual report tool | Report file to upload to the register | Runs inside the e-Business Register portal |
| Payroll | Separate Merit Palk program, free for up to 2 employees | Included, up to 3 employees on Start | 1 employee on Starter, more on Pro | Included |
Prices change
The figures come from each provider’s public price list in November 2026. One Merit Aktiva licence covers up to two companies, while a SimplBooks plan covers one company.
Merit Aktiva
Merit Aktiva is the best-known accounting program in Estonia. Its developer, Merit Tarkvara, says more than 83,000 companies use it, and student surveys of small Estonian companies at Tallinn University of Technology have found it the most widely used. The interface comes in Estonian, English and Russian, statements from LHV, SEB, Swedbank and Coop arrive automatically, and VAT and payroll returns go to the Tax and Customs Board from the program. The Standard plan covers everyday bookkeeping, while the Pro plan adds automatic connections to online shops, payment providers and other software. Payroll runs in a separate program, Merit Palk, which is free for up to two employees, and customer support is free.
SimplBooks
SimplBooks is a Tallinn company whose program is designed for founders who keep their own books; it reports more than 20,000 users. The interface is in Estonian, English and Russian. The Start plan costs less than Merit Aktiva Standard, yet includes payroll for up to three employees, free e-invoices and direct bank connections, so the previous day’s transactions arrive every morning and recurring ones can be booked automatically. Tax returns go straight to the Tax and Customs Board, and the annual report is prepared in a built-in tool. If you only issue invoices and leave the rest to an accountant, the MINI plan is enough.
SmartAccounts
SmartAccounts, also from Tallinn, has a pricing model that suits quiet companies. On the Starter plan you prepay for entries and use them whenever you need, with no monthly fee, which works well for a holding company with a handful of transactions a year. Once the business becomes active, the Pro plan adds direct bank connections, free e-invoices and tax returns sent straight to the Tax and Customs Board. The program also has inventory and fixed-asset modules and connects to Scoro, Envoice and WooCommerce among others. The interface is in Estonian and English only. LHV business clients can use the program free for the first five months.
e-Financials
Known in Estonia as e-arveldaja, e-Financials is run by the Centre of Registers and Information Systems, the state body behind the e-Business Register, and sits inside the same portal, so you log in with an ID card, Smart-ID or an e-Residency card. The interface is in Estonian and English, tax returns are submitted from the program and the annual report is prepared in the register itself. After the free first year, a company with up to 10 entries a month pays €5 a year; with 11 to 50 entries the fee is €5 a month and above 50 it is €9 a month, all plus VAT, according to the e-Financials price list. The trade-off is less automation: bank statements are uploaded as files, and there is no inventory module.
Xero and Other Foreign Software in Estonia
Xero, QuickBooks and similar programs were built for other markets. Xero has country editions for the UK, the US, Australia and a few other countries, but none for Estonia, where companies use its Global edition with a generic sales tax report. In its own product forum, Xero confirms that VAT return filing is supported only for the UK.
For an Estonian OÜ this means double work: the books live in Xero, but the VAT return, payroll tax return and annual report are prepared in the Estonian format elsewhere, usually by an accountant who converts the figures. The Tax and Customs Board itself advises users of foreign software to ask their provider whether it will support Estonian data-based reporting. Xero makes sense mainly when the company belongs to a group that already reports in it.
Xolo, Enty and Other e-Residency Platforms
A separate category is the e-Residency service platforms such as Xolo, Enty or Companio, which bundle their own accounting software with a monthly accounting service. You do not choose a program at all: invoices, bank feeds and reports live inside the provider’s system. That is convenient while you stay, but the books are tied to the provider, and if you change provider they have to be moved into one of the programs above. An accountant who works in a standard program such as Merit Aktiva leaves you free to take your books elsewhere.
Which Accounting Software Is Best for Your Estonian Company
The best accounting software for an Estonian company depends mostly on how active it is and who keeps the books.
| Your situation | A sensible choice |
|---|---|
| Holding or dormant company with a few entries a year | SmartAccounts Starter or e-Financials |
| Freelancer or small service company keeping its own books | SimplBooks Start or Merit Aktiva Standard |
| Company that leaves the books to an accountant | The program your accountant works in, with your own login to issue invoices and see reports |
| Online shop or business that needs integrations | Merit Aktiva Pro, SimplBooks Start or SmartAccounts Pro |
| Company within an international group | The group’s system, with Estonian reports prepared separately |
Whichever you pick, use the free period to enter a month of real transactions before you pay. Moving later means transferring opening balances and unpaid invoices, so the start of a financial year is the easiest moment to switch programs or to hand the books over to an accountant.
Who Works in the Program: You, an Accountant or Both
Software takes care of the routine, but it does not decide how a transaction should be booked, when the company must register for VAT or how a dividend is taxed. Most problems in books that founders keep themselves start there and come to light when the annual report is due. The report itself also needs notes and, for most companies, a management report on top of the figures from the program. There are three ways to divide the work.
| Set-up | What you do | What the accountant does | Suits |
|---|---|---|---|
| You keep the books yourself | Invoices, bank entries, tax returns and the annual report | Nothing, or a one-off check before the annual report | Dormant companies and founders with accounting knowledge |
| You issue invoices, an accountant does the rest | Sales invoices and uploading purchase documents | Bank entries, tax returns, the annual report | Active companies whose owner wants to see sales and balances at any time |
| An accountant runs everything | Sending documents and approving the reports | All bookkeeping and reporting | Owners who do not want to open the program at all |
In the second and third set-ups the program is normally the accountant’s choice, and you only need a login. Our accounting team keeps the books of Estonian companies owned from abroad in this way, mainly in Merit Aktiva: clients who want to stay hands-on issue their own sales invoices, while we handle the bookkeeping, tax returns and annual report. We also take over books kept elsewhere, file the annual report for owners who kept the books alone, and put neglected books back in order.
If you are choosing accounting software for a new Estonian company, send us a short description of your business and we will suggest how to organise its accounting from the start.
Frequently Asked Questions
Student surveys of small Estonian companies have found Merit Aktiva the most widely used program. For a small company, though, SimplBooks, SmartAccounts or e-Financials can be just as suitable and cost less.
Yes. Merit Aktiva and SimplBooks have Estonian, English and Russian interfaces, while SmartAccounts and e-Financials work in Estonian and English. The annual report itself must still be filed in Estonian, which is one reason many owners hand it to an accountant.
Yes. The state-run e-Financials is free for the first year, and afterwards a company with up to 10 entries a month pays only €5 a year plus VAT. Merit Aktiva also has a free version for six months, with limits on the number of invoices and entries.
Yes, for bookkeeping, but neither has an Estonian edition or prepares the Estonian VAT return, payroll tax return or annual report. These have to be prepared separately, usually by an accountant, which means double work.
Yes. You keep the entries during the year, and an accountant checks them, prepares the notes and management report and files the report through the e-Business Register. It costs less than monthly accounting and still catches booking errors before the report is filed.
No. The law makes the management board responsible for the books, and the board may keep them itself. Software only records what you enter, though, so many e-residents and other founders from abroad use an accountant at least for VAT returns and the annual report.
