As a manager, he most notably spent three and a half years with Benfica in Portugal, winning seven major trophies, which included two consecutive Primeira Liga titles, before subsequently having periods in charge at Al Nassr, Spartak Moscow and the Egyptian national team.

[4] During his career, in which he played for five clubs, he never competed in higher than the third division (four seasons), also spending eleven years in the fourth.

[4] After starting as a manager with his main team Vilafranquense, Vitória moved in 2004 to Benfica, spending two seasons with its junior side.

[9] Despite a troubled start, Benfica secured a third Primeira Liga title in a row and 35th overall with a 4–1 win over Nacional at the Estádio da Luz on the final matchday, establishing a Portuguese league record of 88 points in 34 matches.

[11] Moreover, he also managed the team to the quarter-finals of the UEFA Champions League and to their seventh Taça da Liga trophy, beating Marítimo 6–2.

[13] On 23 October 2016, he surpassed Jimmy Hagan's 43-year-old record of 15 consecutive away wins in the league, achieving the 16th as Benfica defeated Belenenses 2–0 away.

The next season, Vitória won the domestic Super Cup[16] and guided Benfica to a second place in Primeira Liga and to the worst Portuguese campaign in the Champions League,[17] which included the club's record loss in the competition, 5–0 to Basel.

[26] Zarema Salikhova, wife of then-co-owner Leonid Fedun, resigned from the board due to her disagreement with the decision.

[30] On 31 October 2024, the Portuguese signed a deal to become the head coach of Greek Club Panathinaikos, until the end of 2026 season.