Your in-house accountant has resigned: how to hand over the work and meet reporting deadlines

When an in-house accountant leaves, it is important to hand over their work to a new specialist in good time. Otherwise, the company risks missing tax return deadlines, losing access to documents or discovering unfinished transactions only after the employee has left.

This article sets out a step-by-step plan for handing over the accounts, checking access permissions and finding a replacement.

How much time does the company have?

When resigning in the ordinary course, an accountant must give their employer at least 30 calendar days’ notice. During a probationary period, the notice period is 15 calendar days. In exceptional circumstances, an employment contract may be terminated without advance notice. These rules are set out in the Employment Contracts Act (Töölepingu seadus, TLS).

The notice period starts on the day after the employer receives the resignation notice.

Example. An accountant gives notice on 1 March and works until the end of the month. In April, the company must submit its TSD return for payments made in March and its VAT return for March. This will have to be done without the former accountant.

An accountant may also leave earlier, for example by mutual agreement or where there are legal grounds for termination without notice. It is therefore best to start the handover as soon as the resignation notice is received, rather than leaving it until the final working days.

What consequences can the company face?

An accountant’s departure does not release the company from filing returns and paying taxes. The main deadlines remain unchanged:

• TSD — by the 10th day of the month following the month in which the payment was made.
• VAT return — by the 20th day of the following month.
• Annual report — within six months after the end of the financial year.

If the filing deadline falls on a weekend or public holiday, it moves to the next working day.

Failure to submit tax returns may result in a fine of up to €3,200 for the company under the Taxation Act (Maksukorralduse seadus, MKS). The Estonian Tax and Customs Board (EMTA) may also order the company to submit the return and apply enforcement measures provided for by law.

If tax is not paid on time, interest accrues on the debt at 0.06% per day.

The company’s management board is responsible for organising its accounting. Even if the accountant leaves unexpectedly, the company must therefore ensure that reports are filed and taxes paid on time.

What to do as soon as the resignation notice arrives

Do not wait until the accountant’s last working day. As soon as you receive the notice:

• Check the upcoming deadlines. Which returns and tax payments are due in the next two months?
• Appoint someone to oversee the handover. Who will receive the documents and monitor unfinished tasks?
• Check access to the accounts. Make sure the company can access its accounting software, documents and essential work systems.
• Start looking for a replacement. A new employee or accounting firm must have time to take over the accounts before the next reporting deadlines.

The earlier you start the handover, the lower the risk of discovering missing documents or unfinished accounting work only after the employee has left.

How to organise the accounting handover

Before leaving, the accountant should hand over their work so that a new specialist can continue. This means obtaining not only the documents but also information about the state of the accounts and any unfinished tasks.

• Accounting documents and data. Invoices, contracts, bank statements, accounting registers and other documents needed to continue the work.
• Information about the state of the accounts. Up to which month the accounts are complete, which transactions have not yet been entered and whether any discrepancies or errors need correcting.
• Unfinished tasks. Unpaid invoices, amounts owed by customers and to suppliers, matters involving the tax authority, and returns that need to be filed or corrected.
• Payroll data. Information about employees, annual leave, sick leave, applicable tax allowances and other circumstances that affect payroll calculations.
• Information about work systems. Which accounting programs and services are used, where documents are stored and which access permissions need to be reassigned.

It is best to record all this in a handover statement. Specify which documents have been transferred, which tasks remain unfinished and up to which month the accounts are complete. The new accountant will then know where to start, and the company will have a record of the state of the accounts at the time of handover.

Under the Accounting Act (Raamatupidamise seadus, RPS), accounting documents must generally be kept for seven years. Check that source documents, contracts and reports are stored in a system accessible to the company, rather than solely in the accountant’s personal email or on their computer.

Which access permissions to revoke when the accountant leaves

By the time employment ends, revoke the former employee’s access to:

• e-MTA. A company representative’s permissions do not end automatically when their employment ends. You must revoke them yourself under “Seaded” → “Pääsuõigused” → “Esindajate pääsuõigused”.
• Online banking. Revoke permissions to view accounts and prepare or approve payments.
• Accounting software and cloud storage. Disable the employee’s individual user account. If shared passwords were used, change them.

Do not give the new accountant the former employee’s personal passwords. Set up access for a new user with the necessary permissions.

If an accountant has left but their representative permissions remain in place, they may still be able to view the company’s tax data and take actions within the permissions granted.

Who will handle the accounts after the employee leaves?

When an in-house accountant leaves, the company needs to decide who will continue keeping the accounts and filing reports. There are three options.

Hire a new in-house accountant. This suits companies that need a full-time specialist. However, finding and hiring an employee can take more than a month, especially if the candidate is still working for another company. Accounting and tax return filing must still be arranged during that time.

Outsource the accounting. An accounting firm can take over without a lengthy recruitment process. The accounts do not then depend on one employee being present: another specialist can cover holidays or sick leave. Read more about the cost of an in-house accountant and outsourcing in “How much does an accountant cost in Estonia?”.

If the company handles many transactions, a mixed arrangement is also possible: an office employee collects documents and deals with day-to-day administrative matters, while an accounting firm keeps the accounts, calculates taxes and submits reports.

For guidance on choosing the right arrangement, read “What kind of accountant does your company need?”.

Frequently asked questions when an accountant leaves

The accountant has left and will not hand over the documents. What should we do?

First, send a written request for the accounting documents and data, specifying a clear deadline. If the matter cannot be resolved, consult a lawyer.

At the same time, start reconstructing missing information using bank statements, documents in the accounting software and copies of invoices from business partners. Do not postpone this work until the dispute with the former employee is resolved.

Can I file the returns myself for now?

Yes. A management board member authorised to represent the company alone receives automatic access to e-MTA and can file returns. If a board member can represent the company only jointly with others, the board members must jointly authorise a representative.

However, submitting the return is only part of the work. Taxes must be calculated correctly, payroll data checked, the basic exemption applied and mandatory contributions taken into account. Any mistakes will have to be corrected later.

The new accountant has found errors made by their predecessor. Who is responsible?

The company is responsible to the tax authority for meeting its tax obligations. Errors in returns must be corrected, and interest may be charged if tax has been underpaid.

During the handover, check the most recent returns against the accounting records. This helps identify potential errors and prepare corrections in good time.

How Finance PRO helps when you change accountants

If an in-house accountant has left, you do not have to wait until you find a new employee. An accounting firm can take over the accounts and handle the next reporting obligations.

Finance PRO has provided accounting services in Estonia since 1998. During the handover, we will check up to which month the accounts are complete, which documents are missing and which returns need to be filed in the near future.

If we find errors or unfinished transactions, we will assess the work required to correct and reconstruct the accounts.

Finance PRO uses a double-check system: a second specialist reviews each accountant’s work. A separate coordinator monitors reporting deadlines.

Has your accountant left, or are they planning to leave? We can help take over the accounts, check their condition and arrange timely reporting. The initial assessment of your situation is free.

Phone: +372 5366 6674

Email: info@fpro.ee

Find out more about our accounting services in Estonia.

Read also

• What kind of accountant does your company need in Estonia: from assistant to chief accountant?
• How much does an accountant cost in Estonia: an in-house specialist or outsourcing?
• How to check an accountant in Estonia in 10 minutes

Information is current as of 11 November 2026. This article is for information purposes and does not replace individual accounting or legal advice. Your circumstances may differ — contact us.