Tomar for 2000–01, re-joining Leiria the following season, being coached by a young José Mourinho and quickly becoming an important first-team member, while also being called by the Portugal under-21 side.

However, in preseason, he suffered a major knee injury that kept him out of action for several months,[5] and went on to only serve as third or fourth option at the northerners; on two rare starts, he netted in a 3–0 win at his former club Leiria[6] and was sent off in the 2008 final of the Taça de Portugal, lost against Sporting.

[7] In July 2008 João Paulo, alongside teammate Cláudio Pitbull, was loaned to Romania's FC Rapid București, joining compatriot José Peseiro whom signed as manager.

[11] On 2 March 2017, after four seasons in the Cypriot First Division in representation of three clubs, the 35-year-old João Paulo returned to his homeland and joined amateurs A.C. Marinhense, where he played mainly as a forward.

[12] Of Cape Verdean descent,[13] João Paulo represented Portugal at the 2004 UEFA European Under-21 Championship and the Summer Olympic Games in the same year.