based on what you are saying you may be eligile to fall under NHR value added taxation.
If you work as a sole entrepreneur you should issue invoices through the “recibo verde” regime.
It doesn’t matter where your clients are located. You’ll be taxated in Portugal if you do your activity there.
So in general you would be taxated for the professional incomes at 20% flat rate (other types of incomes have their own treatment).
If you work from Portugal and invoice your clients from Estonia the portuguese tax authority could claim the icome as produced in Portugal and tax it. So be very careful with that.
Please also bear in mind that professional incomes originated in Portugal also pay social security. So you will have to add the social security burden to the 20%.
Hope this helps