The big Brooklyn courtroom became silent when the verdict was read. There was no visible reaction from Guzmán, facing a compulsory death in prison. He will be sentenced June 25.
The American district director Brian Cogan confirmed the judgments with each of the eight women and the four men on the jury and later told their behavior on the panel "made me very proud to be American."
After the jury left the room Guzman waved and smiled at his wife Emma Coronel, a former beauty queen and courtroom who usually caressed and touched her heart.
"Good thanks," she said when she asked how she felt after the judgment.
The partially sequestered and anonymous jury was discussed about 34 hours over six days.
"We are obviously disappointed with the jury's judgment in the trial of Joaquín Guzmán Loera, but respect the process and the jury's decision," defense lawyer Eduardo Balarezo said. "We faced extraordinary and unprecedented obstacles to defending Joaquín …"
The jury heard testimony of undoubtedly torture and cruel murders, epic corruption at almost every level in Mexico, drug addicts and nude underground flies, gold-plated AK-47 and monogrammed diamond-protected guns.
The case of the prosecution contained 200 hours of testimony from 56 witnesses. Fourteen of these witnesses – mostly recognized drug dealers and cartel associations – collaborated with prosecutors in the hope of reducing their own prison sentences.
There were also surveillance pictures, intercepted phone calls and text messages involving Guzmán, as well as exhibits of blingy firepower and cocaine bricks that released potato bags.
Guzmán, who is once listed on Forbes & Bill's Billionaires List, has long been a happy and almost mythical figure. He fled from a Mexican prison in 2001 in a laundry cart and again in 2015 through a tunnel. After resuming in 2016, he was extradited to the United States to meet US federal charges.
CNN's Maria Santana and Eric Levenson contributed to this report.