Born in Porto da Cruz, Madeira, Pontes coached in the youth ranks of Sporting CP from 1996 to 2005, also managing the reserves for two matches in the third tier in February 2003.
[9] On 8 August 2016, Pontes was appointed as the coach of the Nemzeti Bajnokság I club Debreceni VSC after the resignation of Elemér Kondás.
[14] On 22 May, he left the club with mutual agreement and he was replaced by András Herczeg for the last round against Diósgyőri VTK to escape from the relegation.
[15] On 14 July 2018, Pontes was named the new manager of Spanish Segunda División B side FC Jumilla for the upcoming season.
[18] He returned to interim charge of the club on 3 September after the dismissal of Marcel Keizer,[19] and eleven days later he was given a two-year contract for the post, ahead of his first game.