How to Pay Salaries and Taxes After Registering in the Estonian Employment Register - AMS Group

How to Pay Salaries and Taxes After Registering in the Estonian Employment Register

After registering an employee in Nola Accounting and either you or our accountant have entered this information into the Estonian Employment Register, it is important to properly organize the salary payment and tax process to avoid errors and penalties. Let’s go through the steps to do it correctly.

1. Calculating Salary for Payment

Once employees are registered in the Employment Register, you need to calculate their salary for payment.

If the employment contract does not start on the first day of the month, the employee's first salary will be calculated only for the actual days worked and, therefore, will not be a full salary. The first payment must be made no later than the date specified in the employment contract.

Note that salaries in contracts are stated in gross, not net. For example, if an employee’s contract states a salary of €1,000 gross, the actual payment to the employee will be less. To determine the correct amount to pay, you can either use any salary calculation tool available in Estonia (recommended if you have experience with salary calculations) or contact our support team at support@amsgroup.ee, and we will help you calculate the net salary.

The first salary is typically paid in the following month. For example, if an employment contract starts on 10.02.2025, the first salary will be paid in March 2025. 

Important! Salaries and payments to board members must always be made from the corporate account.

If you want us to send you a salary calculation for your employees each month, please inform us separately by contacting our support team. In this case, you will need to provide us with a monthly Excel sheet containing employees’ working hours and other necessary details. Salary calculation in cooperation with an accountant requires collaboration between the person responsible for work schedules and leave in your company and our chief accountant.

Important Aspects of Salary Payments

  • If, for any reason, you did not pay an employee working under an employment contract, you still need to pay the minimum social tax, even if no payment was made.
  • An employee must receive only one salary payment per calendar month. If you decide to make an additional salary payment within the same month, the tax amount will double. Taxes in Estonia are always calculated based on actual payments made.

2. Paying Taxes

Taxes are paid in the month following the salary payment.

By the By the 10th day of the following month, we:

✔️ Prepare and submit the tax declaration to the Estonian Tax and Customs Board (Maksu- ja Tolliamet). 

✔️ Inform you of the tax amount due via email, along with instructions on how to make the payment.

How to Easily Pay Taxes?

  1. Log in to the Estonian Tax and Customs Board online system.
  2. Find the tax amount listed in the system.
  3. Click the “Pay” button and complete the payment.

Important! Taxes must always be paid from the company’s corporate account, not from a personal account.

3. Repeating the Process Monthly

This process is repeated every month:

1️⃣ If you have chosen the option for us to calculate salaries monthly, we will send you the salary amounts for your employees by the 10th of each month.

2️⃣ You process salary payments for yourself and your employees.

3️⃣ By the 10th of the month following the actual salary payment, you will receive the tax calculation from us and must complete the payment through the Tax and Customs Board.

Note: If salaries remain the same each month (for example, if the company owner is the only employee or employees are only family members), there is no need to recalculate it every month. You can simply repeat the payment. However, at the end of the year, it is important to check whether any legal changes have been made that could affect salary payments in the next year. We recommend consulting us in this case.

Key Points to Remember

✔️ Meet salary and tax deadlines to avoid penalties.

✔️ Always use the corporate account to prevent tax issues and accounting discrepancies.

✔️ For employeesthe process is the same – salary payment comes first, followed by tax payment.

✔️ If the salary remains fixed each month, there is no need for monthly recalculations, but verify any legal updates at the end of the year.

Conclusion

After registering in the Employment Register, you need to:

✅ Calculate the salary yourself or receive calculations from the accountant.

✅ Transfer salaries to yourself and your employees.

✅ Pay taxes through the Estonian Tax and Customs Board.

If you have any questions, our support team is always happy to help!