As you may be aware already there are certain internal issues within SEF (Migration Service) that affect the work of Airports and Air-companies. Lisbon arrivals are experiencing long queues of up to 90 minutes at passport control.
Due to Brexit the same situation is expected in the airports of Faro and Porto starting March 2019.
Please allow for this and manage your time to avoid disappointment. The sunny Algarve is waiting for you!