We have writtten more extensively about taxes in our E-residency guide. Basically, your Estonian company would be automatically considered a tax resident in Estonia. It depends on the tax treaties, if you also need to pay corporate tax in your own country.
e-Estonia Briefing Centre has also written a good article about e-residents’ taxation. And for more specific questions, feel free to get in touch with Estonian Tax and Customs Board (email: nonresident@emta.ee). Although it is highly likely, that they will tell you that you should also consult with a tax advisor in your own country.
If your company’s annual revenue doesn’t exceed €40K, you only need to submit end of financial year reports (by the end of June next year). It’s not obligatory to do that for the first year. If the turnover is more than €40K, you have to do monthly accounting. Fortunately, these services are not very expensive in Estonia. Once you decide on the service provider, most of them can also consult you about international taxes.