El Mencho was captured on Sunday after forces tracked down a romantic partner he was meeting, according to Mexico’s defence secretary.
He was seriously injured in a firefight between his bodyguards and the military commandos deployed to capture him.
El Mencho died while the military was transporting him from the town of Tapalpa, in Jalisco state, to the capital, Mexico City.
At least six of El Mencho’s security guards were also killed in the operation, while three members of the Mexican military were injured, the defence ministry said.
Security secretary Omar Garcia Harfuch said a prison guard, a member of the state prosecutor’s office and 30 members of El Mencho’s criminal organisation were killed in the unrest since his death, according to the AFP news agency.
Mexico’s President Claudia Sheinbaum has praised the army’s operation that led to El Mencho’s death and said her priority is to guarantee peace and security across the country.
“There is calm, there is government, there are armed forces and there is a lot of co-ordination,” Sheinbaum said.
As news of El Mencho’s death spread, members of his cartel launched attacks in many towns and cities where the CJGN is active.