On 1 June 2019, Jesus was appointed manager of Brazilian club Flamengo for a year.
Upon signing, he was met with a negative reaction by fans, former Flamengo players and commentators, who believed that he was too old and could not adapt to Brazilian football; when the team beat opponents, their managers would credit the results to Flamengo's players and finances rather than to Jesus.
He reacted to this atmosphere by saying "I did not come to take anybody's place or to teach anyone.
I am neither better nor worse, I work according to a methodology.
I would like to remind my Brazilian colleagues that we had a Brazilian [manager] in the national team, Scolari.
He was admired by the Portuguese managers.
He and many others who worked in Portugal...All of us in Portugal tried to learn from them, there was never this verbal aggression that there is against me.
I don't understand these closed minds, even from some who are now at home, wearing gloves and shaking".

In his first game on 10 July, the team drew 1–1 at Athletico Paranaense in the first leg of the quarter-finals of the Copa do Brasil.
Four days later in his first Campeonato Brasileiro Série A game, he beat Goiás 6–1 at the Maracanã Stadium.

Jesus' Flamengo won the 2019 Copa Libertadores, defeating Argentina's River Plate 2–1 with a late comeback in the final in Lima, Peru, on 23 November.
He was the first foreign manager to win any international trophy with a Brazilian team, the fifth to win the Copa Libertadores with a foreign club, and only the second European coach, as well as the second non-South American native, to accomplish the feat, after Croatian Mirko Jozić with Chile's Colo-Colo in 1991; he was also only the fourth Portuguese to become club continental champion, following Artur Jorge, Manuel José, and José Mourinho.
Within 24 hours of winning the continental title, Flamengo also won the national championship, when then second-placed Palmeiras lost 2–1 to Grêmio.
He was the second foreign manager, and the first non-South American, to win the Brazilian championship after Argentine Carlos Volante in the debut edition in 1959, the first foreign manager to win it since the round-robin format was introduced, the first manager from his country to win a league title in South America, and the third Portuguese to win a national championship in the Americas, after Guilherme Farinha and Pedro Caixinha.

On 30 December 2019, President of Portugal Marcelo Rebelo de Sousa awarded to Jesus the Order of Prince Henry commander medal (ComIH).
He said that Jesus' achievements aided Portugal's reputation abroad.

On 17 July 2020, Jesus left Flamengo.
He won five trophies with the Brazilian club, winning 43 of the 57 games in charge of the Rubro-Negro.
On 1 June 2019, Jesus was appointed manager of Brazilian club Flamengo for a year. Upon signing, he was met with a negative reaction by fans, former Flamengo players and commentators, who believed that he was too old and could not adapt to Brazilian football; when the team beat opponents, their managers would credit the results to Flamengo's players and finances rather than to Jesus. He reacted to this atmosphere by saying "I did not come to take anybody's place or to teach anyone. I am neither better nor worse, I work according to a methodology. I would like to remind my Brazilian colleagues that we had a Brazilian [manager] in the national team, Scolari. He was admired by the Portuguese managers. He and many others who worked in Portugal...All of us in Portugal tried to learn from them, there was never this verbal aggression that there is against me. I don't understand these closed minds, even from some who are now at home, wearing gloves and shaking".
In his first game on 10 July, the team drew 1–1 at Athletico Paranaense in the first leg of the quarter-finals of the Copa do Brasil. Four days later in his first Campeonato Brasileiro Série A game, he beat Goiás 6–1 at the Maracanã Stadium.
Jesus' Flamengo won the 2019 Copa Libertadores, defeating Argentina's River Plate 2–1 with a late comeback in the final in Lima, Peru, on 23 November. He was the first foreign manager to win any international trophy with a Brazilian team, the fifth to win the Copa Libertadores with a foreign club, and only the second European coach, as well as the second non-South American native, to accomplish the feat, after Croatian Mirko Jozić with Chile's Colo-Colo in 1991; he was also only the fourth Portuguese to become club continental champion, following Artur Jorge, Manuel José, and José Mourinho. Within 24 hours of winning the continental title, Flamengo also won the national championship, when then second-placed Palmeiras lost 2–1 to Grêmio. He was the second foreign manager, and the first non-South American, to win the Brazilian championship after Argentine Carlos Volante in the debut edition in 1959, the first foreign manager to win it since the round-robin format was introduced, the first manager from his country to win a league title in South America, and the third Portuguese to win a national championship in the Americas, after Guilherme Farinha and Pedro Caixinha.
On 30 December 2019, President of Portugal Marcelo Rebelo de Sousa awarded to Jesus the Order of Prince Henry commander medal (ComIH). He said that Jesus' achievements aided Portugal's reputation abroad.
On 17 July 2020, Jesus left Flamengo. He won five trophies with the Brazilian club, winning 43 of the 57 games in charge of the Rubro-Negro.
Jorge Jesus