According to the official report published by Mexican Navy, citizens reported "armed people" in a house at the coastal city of Los Mochis in northern Sinaloa, which was then placed under surveillance for one month. When the gunmen returned to the house, it was raided in the early hours next day, 8 January 2016, by the Mexican Navy's Special Forces with support from the Mexican Army and the Federal Police. The Marines captured Guzmán, along with cartel lieutenant Óscar Iván Gastélum Aguilar ("El Cholo"), following a shootout.
Guzmán and Gastélum managed to escape momentarily through a manhole under the house that led to the city's sewer system, and proceeded to steal a vehicle. Authorities found the whereabouts of this vehicle and it was intercepted. They were then taken to a motel on the outskirts of the town to wait for reinforcements. They were subsequently taken to Los Mochis airport for transport to Mexico City, where Guzman was presented to the press at the Mexico City airport and then flown by a Navy helicopter to the same maximum-security prison from which he escaped in July 2015.
Guzmán had a close call in early October 2015, several days after meeting with Mexican actress Kate del Castillo and American actor Sean Penn. The actress was first approached by Guzman's lawyers in 2014, after having published an open letter to Guzman in 2012 in which she requested him to "traffic in love" instead of in drugs; Guzmán reached out again to del Castillo after his 2015 escape, and allegedly sought to cooperate with her in making a film about his life. On 2 October, del Castillo and Penn visited Guzman for seven hours in his hideout in the mountains, with Penn interviewing the fugitive for Rolling Stone magazine. Guzmán, who had never before acknowledged his drug trafficking to a journalist, told Penn he had a "fleet of submarines, airplanes, trucks and boats" and that he supplied "more heroin, methamphetamine, cocaine and marijuana than anybody else in the world". An unnamed Mexican official confirmed that Penn and del Castillo's meeting helped authorities locate Guzmán, with cell phone interceptions directing Mexican Marines to a ranch near Tamazula, Durango, in the Sierra Madre mountains in western Mexico. The raid on the ranch was met with heavy gunfire and Guzmán was able to flee. The Attorney General of México declared that "El Chapo ran away through a gully and, although he was found by a helicopter, he was with two women and a girl and it was decided not to shoot".
Secretary of the Interior Miguel Ángel Osorio Chong was hosting a reunion with Mexico's ambassadors and consuls when he received a notice from the President on Guzman's capture. He returned a few moments later with Secretary of National Defense Salvador Cienfuegos Zepeda, Secretary of Navy Vidal Francisco Soberón Sanz and Secretary of Foreign Affairs Claudia Ruiz Massieu. Osorio Chong then announced the capture to the diplomats by reading the President's tweet which resulted in applause and chants of Viva México, Viva el Presidente Peña and Viva las Fuerzas Armadas (Long live Mexico, Long live President Peña, Long live our Military Forces). This was followed by a spontaneous rendition of the National Anthem by the crowd.
Colombian President, Juan Manuel Santos, congratulated Mexican President, Enrique Peña Nieto, for the capture of Guzmán. Santos stated that "Guzmán's capture is a success, a great blow against organised crime, and drug trafficking", adding that "finally, this individual (Guzmán), like all criminals, will find what he deserves in the eyes of justice, and we celebrate that the Mexican authorities have recaptured this criminal". Loretta Lynch, United States Attorney General, praised Mexican authorities "who have worked tirelessly in recent months to bring Guzmán to justice".
A renewed process of extradition to USA was formally launched two days after Guzman had been recaptured. Miguel Barbosa Huerta, PRD coordinator in the Senate of México, asked for a trial in México, while Fernando Yunes, PAN senator declared he favored extradition. In the USA, Republican senators Marco Rubio and John McCain called for extradition.