[gituliar]

At first you pay taxes in the country the company you work for is registered (there might be b2b options, which might differ). Then you pay rest in the country where you have a tax residency.

In your example, at first you pay taxes in Germany and if Estonian taxes are bigger, you pay the difference there.

[Archelaos]

I am partly working for an Italian company from Germany. Billing is very simple. I invoice the Italian company according to the so-called reverse charge procedure: My invoice does not include VAT, but only the European VAT number of my and the customer's company. The customer must settle the VAT with his tax office. I only have to inform my tax office at regular intervals about the turnover with the individual companies, so that the European tax authorities can check whether the customer has declared his taxes correctly.

I invoice via my own company. But this is not mandatory. You can also apply for a VAT number as an individual and follow the same procedure. I did this before I set up the company.

[gituliar]

This is because you run your own company. Things are different if one works for a company as an employee.