Pedro Emanuel subsequently became a manager, leading three teams in his country's top flight as well as working in Cyprus, Saudi Arabia, Spain and the United Arab Emirates.

Benfica seemed closer to clinching a deal, but it was FC Porto, under the guidance of José Mourinho, who signed Pedro Emanuel.

[6] In the season following the departure of Mourinho, Pedro Emanuel still managed to appear in the spotlight, as in the 2004 Intercontinental Cup win against Once Caldas, where he scored the decisive penalty, becoming the last player to touch the ball in the competition's history.

He missed the entire following season due to injury,[8] but returned to the starting lineups the following campaign, helping with 19 league appearances as Porto were crowned back-to-back champions.

[13] In July 2010, Pedro Emanuel returned to Porto's main squad, being named assistant manager to newly appointed André Villas-Boas.

He also led the side to their first Taça de Portugal since 1939, notably defeating former club Porto 3–0 at home in the fourth round[16] and Sporting in the final (1–0).

[19] On 10 June 2015, Pedro Emanuel moved abroad for the first time in his career, taking over at Apollon Limassol FC of the Cypriot First Division; his team already included three compatriots.

[27] Pedro Emanuel returned to the Middle East on 5 January 2020 when he was appointed on an 18-month deal at Al Ain FC in the UAE Pro League.

[29] At the start of October 2021, Pedro Emanuel went back to the Saudi main division, to take over at third-place Al Nassr FC until the end of the season.