[throw130]

Is it ok to operate an Estonian company from Germany though?

Not for tax reasons (assuming you would pay the same tax for either a German or Estonian company as others said in the thread) but for bureaucracy reasons. Skipping the whole German procedure.

[sparkling]

It is "okay", but you will end up with more bureaucracy. If, as mentioned, you are living in Germany 99% of the time and spend close to zero time in Estonia, the german tax authorities will (sooner or later) argue that the company is effectively being managed from Germany. Then you have to deal with tax nonsense in two countries and finding a tax consultant who will deal with this is rather expensive. Some basics (if you understand German), are explained here: https://www.ihk-berlin.de/blob/bihk24/Service-und-Beratung/r...