In 2008, Sequeira was appointed manager of Portuguese third division side
Arcos de Valdevez after managing the youth academy of
Braga in the Portuguese top flight. In 2009, he was appointed manager of Portuguese second division club
Aves. In 2012, he was appointed manager of
Famalicão in the Portuguese third division. In 2013, Sequeira was appointed manager of Portuguese second division team
Trofense. After that, he was appointed manager of
Merelinense in the Portuguese fourth division, helping them achieve promotion to the Portuguese third division. In 2017, he was appointed manager of Portuguese third division outfit
Freamunde. After that, Sequeira was appointed youth manager of
Al Nassr in Saudi Arabia. In 2021, he was appointed manager of Uzbekistani side
Lokomotiv (Tashkent). ==References==