He was recaptured several months later - his third arrest in 23 years - in the Sinaloa coastal city of Los Mochis and extradited to the US about a year later.
Guzman, who has been held in solitary confinement for the last two years, pleaded not guilty to the slew of charges, thus beginning his long-waited criminal trial in November.
A jury whose members' identities were kept secret as a security measure reached a verdict after deliberating six days in the expansive case.
The prosecution's case against Guzman, a roughly 5½-foot figure whose nickname translates to "Shorty", included the testimony of several turncoats and other witnesses.
A string of former workers gave evidence against Guzman, 61, with one telling how he shot a man and ordered him to be buried while still alive.
One of the world's most notorious drug lords, Joaquin "El Chapo" Guzman, is on trial in NY and a star witness just revealed a lot about Chapo's Canadian operation.
U.S. District Judge Brian Cogan lauded the jury's meticulous attention to detail and the "remarkable" approach it took toward deliberations.
Guzman's lawyers did not deny the defendant's charges but argued that he was the victim of government witnesses who were worse than he was. "Once that door is open, it can't be closed again", he said. In 2009, Forbes Magazine put him on its list of the world's richest people, with an estimated $1 billion. Imprisoned in Mexico in 1993, he escaped in 2001 hidden in a laundry cart and spent the following years moving from one hideout to another in the mountains of Sinaloa, guarded by a private army. He was finally recaptured in January 2016.
Outside the court, U.S. Attorney Richard Donoghue called it a "day of reckoning", promising the government would continue to root out cartel-related drug-running and corruption.
Together, they are the biggest producers of drugs sold on USA streets.