Pedro Emanuel was born in Luanda, Portuguese Angola. After three seasons as a professional in Portugal's secondary leagues, with F.C. Marco, A.D. Ovarense and F.C. Penafiel, his performances caught the eye of scouts from Porto club Boavista FC, where he had already played as a youth. During his six-year stay in the team he played a large part in the defensive wall – with fellow stopper Litos, fullbacks Nuno Frechaut and Erivan and goalkeeper Ricardo – that led them to the historical Primeira Liga title in 2001; after Litos left for Málaga CF he captained the team for one season, but a move to a larger club was close.