A new residence permit will be issued to UK nationals who are resident in Portugal before 31st December 2020 and replaces the EU residency certificate. The current EU residency certificate will be accepted after 31st December 2020 and until the new residence permit is issued.
If you already have an EU Residency certificate, you can register for a new residence permit now. For this, you will need to register on the SEF Portal at the following link:
https://brexit.sef.pt/en/guia/
Once you have done this, you can download a document which can be printed and used when travelling to prove residence in Portugal.
You will be asked at a later date to book an appointment to provide your biometric data (photo, signature and fingerprints) for your new residence permit.
SEF’s website explains that the registration to exchange your residence document on this Portal will be open until at least the end of June 2021. Thereafter you will need to schedule an appointment directly with SEF to exchange your residence documentation.