Best known for his spell at Benfica, for which he appeared in 318 official games over the course of eight-and-a-half seasons, scoring 58 goals. He was also a leading figure for the national team during the better part of the 1980s and, after retiring, he embarked on a lengthy spell as coach.
After falling out of favour with the club's management, Manuel moved in January 1988 to Switzerland with FC Sion. Only five months later, he returned to the Portuguese capital after signing with Sporting Clube de Portugal. After a solid first season his career began winding down, and he finally retired midway through the 1993–94 campaign, whilst at G.D. Estoril Praia – he had previously represented Boavista Futebol Clube for two years; he was chosen by Portuguese sports newspaper Record as one of the best 100 Portuguese football players ever.
After retiring at 36, Carlos Manuel took on coaching, having managed with little success a host of clubs, mainly in the Lisbon area. Midway through 1997–98, he bought out his contract at S.C. Salgueiros and joined Sporting, but the Lions could only finish fourth and he was sacked, a fate he met mere months after at S.C. Braga.
After the 1986 World Cup loss to Morocco, with the national side being ousted in the group stages – the competition was also stained by the Portuguese players' involvement in the Saltillo Affair – Manuel retired from the international scene, at only 28.