Born in Viseu, Rui Miguel began playing for hometown's Académico FC, first appearing as a senior in the third division.

[1] Rui Miguel moved to the Primeira Liga in the following season, with Associação Naval 1º de Maio.

However, in January 2007, he moved to Poland and signed with Zagłębie Lubin;[4] he returned to his country one and a half years later, where he finally would make a name for himself in the top flight, first with F.C.

[6] Never an undisputed started except for the league's final games (four of his five goals came during that stretch), he contributed solidly as the Guimarães-based team finished sixth and nearly qualified for the UEFA Europa League, for example scoring a last-minute equaliser against eventually fourth-placed Sporting CP (1–1, at home).

[7] After two seasons in Minho and 51 official appearances, Rui Miguel signed for Russian club FC Krasnodar.