Early career Shortly after retiring, Mohamed took up coaching at his last club Zacatepec in the
Ascenso MX, reaching the
semifinals of the Liguilla and leaving the club after they changed name to Leones de Morelos. He took over
Liga MX side
Monarcas Morelia on 23 February 2004, replacing
Rubén Omar Romano. Mohamed was sacked by Morelia in June 2004, after only 13 matches. He subsequently took over
Querétaro in the second division before replacing
José Luis Trejo at the helm of
Chiapas in February 2005. Mohamed was relieved of his duties in April 2005, and was subsequently replaced by
Fernando Quirarte. He subsequently returned to his first club Huracán, achieving a top tier promotion in
2007. Mohamed resigned in September 2007, and returned to Mexico in the following month after being named
Veracruz manager. He resigned the following 27 January, after only eight matches. On 19 March 2008, Mohamed was appointed in charge of
Colón de Santa Fe back in his home country. In September 2010, after attracting the interest of major clubs in the country, he resigned.
Independiente On 4 October 2010, Mohamed was confirmed as new manager of
Independiente. In December, he led side that won the
Copa Sudamericana tournament, defeating Brazilian side
Goiás 5–3 on penalties in the
finals. Mohamed announced his resignation from the club on 4 September 2011, after a poor start of
the season.
Tijuana Mohamed would return to Mexico in 2011, and on 19 September of that year, he was announced as the new manager of recently promoted
Club Tijuana, replacing
Joaquín Del Olmo. He led Tijuana to the
Apertura 2012 championship, the first in the club's history, after defeating
Toluca 4–1 on aggregate in the finals. Mohamed stepped down as Tijuana manager in 2013, so he could move back to Argentina to be closer to his family,
Return to Huracán Shortly after leaving Tijuana, Mohamed became the manager of Huracán for a second time on 2 July 2013. He resigned from the club in October, after three wins and seven losses in ten matches.
Club América On 10 December 2013, Mohamed was named the new manager of
Club América for the
Clausura 2014 tournament after club president
Ricardo Peláez confirmed it during an interview with
Univisión. He was officially presented to the press on 17 December. At the press conference it was revealed that he had signed a one-year contract with the club, with the potential for an extension pending a review of his performance. Mohamed also spoke of the pressure that came with managing América and comparing it to his time with Club Tijuana, saying, "Here I have everything [
sic] to lose." His first two signings where
Paraguayan center-back
Pablo Aguilar, whom he coached while at Tijuana, and
Argentine striker
Andrés Ríos. Mohamed's first league match with América came on 4 January 2014 in a 3–0 victory over
UANL at the
Estadio Azteca. Mohamed suffered his first defeat as América manager on 10 January in a 0–1 loss to Tijuana. Following three consecutive victories against
León,
Atlas, and
Atlante, América suffered defeats to
Pachuca and
Morelia, both 0–1, the first time they had lost back-to-back games since the
Clausura 2012 tournament. The team was criticized for its defensive style of play, with many drawing comparisons to predecessor
Miguel Herrera's more offensive-minded tactics and his successful reign at the club, though some believed that a lack of a proper pre-season and the club being in a period of transition were the reasons for the team's poor performances. On 23 February, América were defeated 1–3 by
Pumas in the
Mexico City derby, ending the club's two-year hegemony over their intracity rival. On 27 April, following a 1–1 draw at Toluca, América secured their qualification for the playoffs. They would ultimately be eliminated in the quarterfinals by
Santos Laguna with a 6–6 aggregate score (América won the first leg 5–3, but lost the second 1–3), with the
away goals rule deciding the series. Going into the liguilla, America's form had dropped significantly and many analyst did not see America making it past the first round. Tensions rose dramatically once America advanced to the semifinal after a nail-biter quarterfinal against Pumas. A few days before the first leg of America's semi-final match against Monterrey, Mohamed dismissed club co-captain
Paul Aguilar after an undisclosed locker room incident. During that week, multiple sources said Mohamed would no longer continue at the club regardless of the playoff result. The club morale was further affected once players
Luis Angel Mendoza and
Jesus Molina were confirmed to be transferring teams before playoffs had ended. On 6 December 2014, Mohamed announced his departure from the club after the end of the Apertura tournament. He still led the club to the Finals, and lifted the Apertura title after defeating UANL 3–1 on aggregate.
Monterrey On 16 February 2015, after the release of
Carlos Barra as coach,
Monterrey appointed Mohamed as their new manager. He made his debut at the helm of the club five days later, in a 2–1 a victory against
Querétaro. Mohamed remained in charge of the
Rayados in the following seasons, taking the club to the
CONCACAF Champions League twice (2016 and 2018), but still being knocked out by Panamanian side
Árabe Unido in the
2016–17 group stage. On 7 May 2018, he resigned.
Celta On 22 May 2018, La Liga club
Celta de Vigo appointed Mohamed as manager on a two-year contract. He was sacked on 12 November, with the team in 14th after 12 matches.
Fourth spell at Huracán On 28 December 2018, Mohamed returned to Huracán, starting his fourth spell as manager of the club. He resigned the following 23 April, after the club was knocked out of the
2019 Copa Libertadores.
Return to Monterrey On 9 October 2019, Mohamed returned to Mexico and Monterrey, after being named in charge until the end of the season. On 25 November of the following year, he left on a mutual agreement.
Atlético Mineiro On 13 January 2022, Mohamed was appointed as manager of
Atlético Mineiro of Brazil. On 20 February 2022, Mohamed won his first title with the club, by beating
Flamengo in the penalty shootouts of the
Supercopa do Brasil match. On 2 April 2022, Mohamed won his second trophy with Atlético, beating arch rivals
Cruzeiro in the
Campeonato Mineiro final with a 3–1 score. He left the club on 22 July 2022, following a string of poor results in the
Campeonato Brasileiro and an exit in the round of 16 of the
Copa do Brasil.
UNAM In March 2023, Mohamed returned to Mexico, this time as manager of
UNAM. He transformed the team into a consistent side in the
Apertura 2023 tournament, but they were eliminated in the semifinals at the hands of
Tigres UNAL due to them being the higher seeded team in the regular season after the tie ended 1-1 on aggregate with neither team scoring any away goals. On 12 December 2023, Mohamed stepped down from his position citing personal reasons.
Toluca On December 11, 2024, Mohamed was appointed head coach of
Toluca. Within six months, the club won their 11th league championship, ending a 15-year title drought. On December 14, 2025, Toluca claimed their 12th league title, defeating Tigres to secure a back-to-back championship. ==Personal life==