I don't know anything about Belgium but it's probably similar: If you have a branch located in Germany (which is definitely the case if you are the sole employe

I don't know anything about Belgium but it's probably similar: If you have a branch located in Germany (which is definitely the case if you are the sole employee permanently living there) you need the pay the same taxes as an equivalent German company for all income derived from there. The Belgian tax authorities must allow you to invoice from the Estonian company (that's part of EU freedoms) but it probably won't save you much taxes.