If you live in Germany and pay yourself a salary from an Estonian company, then you will only pay taxes in Germany and no taxes in Estonia.

The 20% Estonian corporate tax does not apply to salaries for non-residents, but for things like dividends.

P.S. Leapin is a company that specializes in accounting for online businesses looking to establish a presence in Estonia. You can find some more info on this stuff on their website:

https://www.leapin.eu/faq/receiving-funds#what-taxes-do-i-ne...