De Deus started working as a coach immediately after retiring, working with Vitória de Setúbal in the fitness department under
José Couceiro and
José Rachão; he also had a spell with
G.D. Interclube in Angola, again as a fitness coach. His first job as a manager was with the
Cape Verde national team, which he left after an unsuccessful
qualification campaign for the
2010 FIFA World Cup; shortly before the tournament, he led the team to a goalless
friendly draw against
Portugal in
Covilhã. In the summer of 2010, and without permission from the
Cape Verdean Football Federation, de Deus was appointed at
Segunda División B club
AD Ceuta. He was sacked by the Spaniards before the end of the year, however, returning to Portugal and joining
S.C. Farense, which he could not
prevent from being relegated from the
third level in spite of an incredible comeback. From 2011 to 2013, de Deus worked in Portugal's second tier, with
Atlético Clube de Portugal and
U.D. Oliveirense. For the
2013–14 campaign he was appointed at
Gil Vicente FC, thus making his debut in the
Primeira Liga. After a poor start to
2014–15, which saw the team lose the first three league matches, de Deus was relieved of his duties. On 6 October, he was hired by
Sporting CP B on a one-year contract with the option of a second. He was sacked on 15 February 2017, after a 2–1 home loss to
Varzim S.C. put
the reserves into second-last place. On 21 March 2017, de Deus returned to the top flight with
C.D. Nacional, becoming the third manager of the season for the last-placed side. He left on 24 May, after their relegation in the same position. De Deus was hired at
Indian Super League franchise
NorthEast United FC on 17 July 2017. The team from
Guwahati dismissed him the following 2 January, having won once and scored twice in seven games. Having already assisted him at
Al Hilal SFC in Saudi Arabia, de Deus was one of six compatriots that Portuguese manager
Jorge Jesus named in his staff at Brazilian club
Clube de Regatas do Flamengo in June 2019, being appointed assistant along with Tiago Oliveira. In November, as Jesus was suspended, he led the team in the 3–1 home win against
Esporte Clube Bahia for the
Série A as an
interim, being chosen the round's best coach. De Deus followed Jesus to
S.L. Benfica in 2020; the following 28 January he covered the ill manager's absence in a 3–1 home win over
B-SAD in the
quarter-finals of the
Taça de Portugal. On July 1, 2023, Al-Hilal announced the reappointment of Jorge Jesus as their manager for the 2023–24 season. The coach's staff members, including João de Deus, accompanied the coach in his return to the Arab team. ==Managerial statistics==