Early years Fonseca started coaching immediately after retiring, remaining two years at the helm of Estrela da Amadora's youths. In
2011–12, Fonseca was appointed at
Aves in division two for his first job in the professionals, and he led the team to the third position, just two points shy of promotion.
Paços Ferreira In his
first season in charge of a top-flight team, Fonseca led
Paços de Ferreira to a third-place finish after signing a two-year contract on 28 May 2012. The club consequently
qualified for the play-off round of the
UEFA Champions League for the only time in its history; in the domestic league, they only lost to champions
Porto and runners-up
Benfica, notably winning both games against
Braga (2–0 at home, 3–2 away) and
Sporting CP (1–0 on both occasions). Paços also reached the
semi-finals of the Portuguese Cup that campaign, being knocked out by Benfica.
Porto Fonseca succeeded
Vítor Pereira at Porto – winners of the last three league titles – when he joined on a two-year deal on 10 June 2013. He started his spell on a high note, winning
the year's
Supertaça Cândido de Oliveira after a 3–0 victory over Vitória de Guimarães which marked his first honour as a coach. However, on 5 March 2014, following a string of poor results that left the club in the third position in the league,
nine points behind leaders Benfica, Fonseca was relieved of his duties. Previously, on 12 January, he had stated that Porto would be champions in the last matchday against that opponent.
Paços return and Braga On 11 June 2014, Fonseca returned to Paços de Ferreira. His
one season back at the
Estádio da Mata Real resulted in an eighth-place finish, missing out on
qualification for the
UEFA Europa League on the final day. Fonseca agreed to a two-year contract with Braga on 1 July 2015. He led them to
fourth position, also
winning the domestic cup for the first time in 50 years with a
penalty shootout victory over Porto in the
final. In the Europa League, they reached the
last-eight stage. He won
the double in all three seasons of his spell– which earned him the distinction as the league's best coach in
2016–17. Fonseca's side reached the
round of 16 of the
2017–18 Champions League, after finishing second in the group stage following a 2–1 home defeat of
Premier League club
Manchester City. Having inflicted a first defeat in 29 matches of
Pep Guardiola's side, he kept a promise to do his next press conference dressed as the fictional hero
Zorro.
Roma On 11 June 2019, Fonseca was appointed manager of
Roma. He led the side to the fifth place in the
Serie A in his
first season, as well as the
semi-finals of the subsequent Europa League. He announced his departure in May 2021. Immediately after leaving Roma, Fonseca was director
Fabio Paratici's top choice to be manager of
Tottenham Hotspur, but the advanced negotiations were scrapped on 17 June 2021, allegedly due to tax issues. However, in an interview with
The Daily Telegraph in September, the former revealed that the main reason for this was that the latter wanted to hire a more defensive-minded coach. In October, he was interviewed by
Newcastle United following their
Saudi-led takeover, before the interest shifted to
Unai Emery and
Eddie Howe; his name was then linked to a third English club,
Aston Villa.
Lille On 29 June 2022, Fonseca signed a two-year contract with French
Ligue 1 club
Lille. He made his debut on 7 August in a 4–1 home win over
Auxerre. On 9 October, his team defeated
Derby du Nord rivals
Lens 1–0 also at the
Stade Pierre-Mauroy. One of the best attacking sides in the first half of
that season, they played an open
4–2–3–1 formation with
Benjamin André,
André Gomes or
Angel Gomes being deployed as
central midfielders behind playmaker
Rémy Cabella and lone striker
Jonathan David. Following a 4–3 home victory against
Monaco on 23 October, only
Lyon and
Paris Saint-Germain had more possession in the domestic league. In the
2023–24 campaign, Lille finished fourth after a 2–2 draw with
Nice on the final matchday, thereby missing out on direct
Champions League qualification. He left on 5 June 2024 by mutual consent.
AC Milan On 13 June 2024, Fonseca was appointed as the new head coach of
AC Milan, agreeing to a three-year deal as of 1 July. After a bad start in the season and rumours of imminent dismissal, he oversaw a 2–1 victory against
Inter Milan in the
Derby della Madonnina on 22 September. Ahead of the match, he experimented with the lineup, choosing 4–4–2 and 4–2–4 for defence and attack, respectively; it was also the first time the club had defeated this opposition in two years, ending a six-game losing streak. Fonseca was sacked on 29 December 2024, with the team in eighth position.
Lyon On 31 January 2025, Fonseca returned to the French top tier with Lyon. On 2 March, he aggressively confronted
Benoît Millot at the end of a 2–1 home win over
Brest, his head making contact with the
referee; he was
sent off for his actions and, the following day (his 52nd birthday), handed a suspension until 30 November that included the impossibility of sitting on his team's bench or entering their dressing room until 15 September. ==Managerial style==