The jury found Guzman guilty on 17 counts that covered a range of drug crimes related to narcotics trafficking and conspiracies to kill rivals.
Law enforcement officials said that he'll be looking at a mandatory life sentence without parole.
El Chapo escaped from Mexican prisons twice, but was recaptured in 2016, and extradited to the USA in January 2017.
Guzman staged two dramatic escapes from Mexican high-security prisons and cultivated a Robin Hood image among the poor in his home state of Sinaloa. Unlike other people in a similar position, Guzman would not plead guilty and went for a public trial after being extradited to the US. Many described Guzman's willingness to use violence against enemies of a cartel that prosecutors say smuggled at least 181 metric tons of cocaine into the U.S. over two decades.
Known as one of the most notorious and infamous drug traffickers in modern history, Guzman managed to evade authorities and broke out of Mexican prisons twice.
The defence case lasted just half an hour.More news: Gordon Banks dies 2019 at age 81 - Obituary
Deliberations were complicated by the trial's vast scope. Peña Nieto denied it, but the allegation fit a theme: politicians, army commanders, police and prosecutors, all on the take. The same day, he grinned broadly at audience member Alejandro Edda, the Mexican actor who plays Guzman in the Netflix drama "Narcos".
But his sing-songy voice filled the courtroom, thanks to recordings of intercepted phone calls.
One of the trial's most memorable tales came from girlfriend Lucero Guadalupe Sanchez Lopez, who testified she was in bed in a safe house with an on-the-run Guzman in 2014 when Mexican marines started breaking down his door.
They heard how Guzman made a name for himself in the 1980s as "El Rapido", the speedy one, by building cross-border tunnels that allowed him to move cocaine from Mexico into the United States faster than anyone else.
Asked what he was wearing, she replied: "He was naked. He left us behind". He then got an escort from crooked police officers into Mexico City before retreating to one of his many mountainside hideaways.
This came after his second, short-lived escape from prison. "In front of you".