The turnover threshold for mandatory VAT registration in Estonia is EUR 40 000 from the beginning of a calendar year. If your annual taxable supply is below EUR 40 000, then you have no obligation to register as a person liable for VAT and you are not required to calculate and pay VAT in Estonia on the provided services, which would otherwise be taxable.
A voluntary registration before reaching the registration threshold is also possible. In this case, the Estonian Tax and Customs Board needs to be provided with sufficient evidence (normally a business plan) that proves the intentions of starting and running a business. The Estonian tax authorities may refuse VAT registration if there are no transactions with clients located and operating in Estonia.
Detailed information about VAT can be read from the Estonian Tax and Customs Board´s e-Residency page here.