Manuel began his managerial career in 2003 with his hometown, Esmoriz-based side, S.C. Esmoriz. He worked for a span of three years with the U-11 and U-13 squads of the Esmoriz-based club.
Later in 2005, he moved to São João da Madeira where he was appointed as the head coach of the U-12 side of A.D. Sanjoanense. Impressed with his performances with the junior side he was then promoted as the assistant manager of the first team squad of the club in 2006 where he worked under Jorge Castelo. During this time he also played the role of a scouting coordinator for the club till 2008. In 2007, he was appointed as the head coach of the U-13 side, helping them win the Aveiro district championship. Impressed with his achievements, he was then promoted as the head coach of the U-15 side which participated in the Campeonato Nacional de Juniores C, helping his side qualify for the second stage of the championship for the first time in the club's history. In 2009, he began working as the head coach of the U-19 side which participated in the Campeonato Nacional de Juniores A. In the 2010-11 season, he also worked as an assistant to José Brito of the first team of the club helping them win the championship and super cup in the particular season. In the meantime, he began working as a scouting coordinator for Portuguese club FC Porto in Aveiro region. Impressed with his six-year long work with various junior sides and as an assistant, the São João da Madeira-based side appointed the young Portuguese as the head coach of the first team side for the 2011-12 season.
He first moved out of Portugal in 2012 to the Middle East and more accurately to Oman where he was appointed as the assistant manager of Oman Professional League side, Al-Nahda Club. He helped the Al-Buraimi-based side achieve the runners-up position in the most prestigious tournament of the nation, Sultan Qaboos Cup in 2012-13 and 2013-14. He also helped his side become the winners of the inaugural Oman Professional League in 2013–14 Sultan Qaboos Cup. Participating in the 2014 GCC Champions League, he helped his side qualify for the Semi-finals of the competition where the Omani club lost 3-2 on aggregate to Emirati club Al-Nasr SC.
On 18 July 2016, he was appointed as the manager of 2015–16 Oman Professional League champions, Fanja SC. He made his Oman Professional League debut as the manager of the defending champions on 17 September 2016 in a 3-1 win over newly promoted side, Ja'alan SC. However, a disappointing run in the league Fanja's management decided to part company with the Portuguese.
Dhofar
On 1 January 2017, he was appointed as the manager of Dhofar S.C.S.C.