José Pedro Pontes is a member of the Associação Portuguesa para o Desenvolvimento Regional (APDR), the Portuguese branch of RSAI. He was Editor of the Portuguese Journal Estudos de Economia between 1996 and 1999. He belongs to the Editorial Boards of other two Portuguese journals: GeoInova and Revista Portuguesa de Estudos Regionais. He has organized three Workshops: "Regional Development in Europe" in ISEG in 1998; "Workshop on Game Theory and Applications" in 2001 (together with João Gata) in ISEG in 2001; and the "Luso-Japanese Workshop in Geographical Economics" (together with Masahisa Fujita) at the Convento da Arrábida in 2004.

José Pedro Pontes has received the prize of Fundo de Investigação do ISEG (FISEG) for publication of articles in refereed journals in five successive years: 2001, 2002, 2003, 2004 and 2005.