Alves became a coach after finishing his player career, managing Boavista on three separate occasions, C.F. Estrela da Amadora (leading the Amadora team to an historical 1990 Cup of Portugal triumph), Vitória de Guimarães, C.F. Os Belenenses, Salamanca, S.C. Campomaiorense, S.C. Farense, Académica de Coimbra and Leixões SC.
After three years out of coaching, he returned to Benfica in 2007, to be in charge of its under-18 team.