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. Estonian tax authority may refuse VAT registration if there are no transactions with clients located and operating in Estonia.
A detailed information about VAT can be read from the Estonian Tax and Customs Board´s e-Residency page here.