In the United States, decades of smuggling activities by the Sinaloa Cartel led to indictments of Guzmán and his associates across Chicago, San Diego, New York City, New Hampshire, Miami, and Texas.

[6] This 2009 indictment originally charged Guzmán alongside his associate Ignacio Coronel Villarreal, Cartel co-leader Ismael "El Mayo" Zambada García and his brother Jesús "El Rey" Zambada García, as well as brothers Arturo and Héctor Beltrán Leyva of Sinaloa Cartel allies-turned-enemies the Beltrán-Leyva Organization.

[13] Thus by the fourth (and final) superseding indictment of May 2016, Guzmán's sole codefendant was Ismael "El Mayo" Zambada, who remains at large.

[15] After a manhunt by Mexican authorities led to an arrest in 2014, escape in 2015, and recapture in 2016, Mexico formally launched a renewed process of extradition to the United States.

[20] Mexican President Enrique Peña Nieto did not have the authority to issue an executive order to immediately extradite Guzmán without due process.

[21] A critical requirement for extradition was that the United States's agreement not to seek the death penalty against Guzmán if he was found guilty of homicide charges.

[2][22][23] Guzmán was transferred on May 5, 2016, to a prison near Ciudad Juarez, near the border with Texas,[24] and Mexico expected to extradite him to the United States by February 2017.

[25] On October 16, Vicente Antonio Bermúdez Zacarías was assassinated while jogging near Mexico City; he was a federal judge involved in Guzmán's extradition proceedings.

[27] The Mexican Government said in a formal statement, "The government of the Republic announces that today the Fifth Appellate Criminal Court in Mexico City ruled to deny the protection of the Federal Justice system to Joaquín Guzmán Loera against the agreements made by the Ministry of Foreign Affairs on May 20, 2016, which permitted his extradition to the United States of America in order to be tried for various crimes, after finding that those agreements complied with constitutional requirements, the requirements of bilateral treaties and other legal rulings that are in effect and that his human rights were not and have not been violated by these proceedings".

The charges included money laundering, drug trafficking, kidnapping and murder in Chicago, Miami, New York and other cities, and with various associates as co-defendants.

[37] Acting United States Attorney General Sally Yates called him the "alleged leader of a multi-billion dollar, multi-national criminal enterprise that funneled drugs onto our streets and violence and misery into our communities".

[38] In their memorandum of law arguing for remand, the United States Attorney for the Eastern District of New York introduced evidence of the Sinaloa Cartel's narcotrafficking including photographs of seized drugs, vehicles, and weaponry and stated that, "Given Guzman's prior history, unless Guzman is incarcerated under the strictest security arrangements, the risk of his continued criminal activity is certain."

[60] Among these were cooperating witnesses from the Colombian and Mexican cartels detailing the operations and extent of the narcotics trade: On February 1, 2019, one day after the closing arguments, court documents were unsealed that alleged that Guzmán regularly had sexual relations with girls as young as 13, drugging them prior without their knowledge.

[78] After the session concluded, Guzmán smiled and waved at his wife Emma Coronel Aispuro with a thumbs-up; she said that she was fine when asked how she was doing, and then left the courtroom.

"[80] U.S. Attorney Richard Donoghue spoke to the press and said that this conviction was a success for the U.S. and Mexico, including the families affected by drug violence and substance use disorder.

[79] The first count on which Guzmán was convicted—operating a continuing criminal enterprise—included 27 separate violations and was the most significant charge in the indictment, as it carries a mandatory sentence of life imprisonment.

The jury found Guzmán guilty of 25 of the 27 listed predicate offenses that formed the basis of the continuing criminal enterprise charge.

[90] One revealing detail was that they claimed was that at least five jurors violated the judge's order to refrain from researching Guzmán in the news and in social media during the trial, and of talking about the case with each other when they were not in court time.