But finding him after they raided one of them was trickier than they thought.
"This particular house had bars on the windows. The front door was reinforced, and was so difficult to get in, it was like 10 minutes went by," said Derek Maltz, who once led the Drug Enforcement Administration's special operations division.
The time it took Mexican marines to get past the reinforced steel doors was enough to allow Guzman to escape. His route? A hidden hatch under a bathtub.
The nearest safe house was 3 kilometers (almost 2 miles) away, but thanks to the network of tunnels, Guzman was able to slip out of sight once again.
They nabbed him later in a beachside hideaway in Mazatlan, a resort city about 200 kilometers (125 miles) away.
2015: Prison break
But he wouldn't remain behind bars for long. Just 14 months after Guzman landed in Mexico's maximum-security Altiplano prison, he broke out in July 2015.
After Guzman's getaway, authorities said they made a shocking find underground: a lighted and ventilated tunnel, replete with tracks and a modified motorcycle inside.
The tunnel, Mexican National Security Commissioner Monte Alejandro Rubido said
, began with a 50 x 50 centimeter (20 x 20 inch) opening inside a shower in Guzman's cell.
That opening, officials said, connected to a vertical passageway going about 10 meters (33 feet) underground.
The passageway, outfitted with a ladder, led to a tunnel that was about 1.7 meters (5.5 feet) tall and more than 70 centimeters (28 inches) wide.
Inside the passageway, investigators found what Rubido described as an "adapted motorcycle on tracks that was likely used to remove dirt during the excavation and transport the tools for the dig."
In one respect, the tunnel was notably different from others Guzman's Sinaloa cartel had built.
"It was arrow straight," said Jim Dinkins, the former head of investigation for the U.S. Department of Homeland Security. It was a sign, Dinkins said, that a cartel known for building sophisticated tunnels to send drugs across the U.S.-Mexico border had tapped its best and brightest for help.
"Look -- the boss, El Chapo, is in prison. You're not going to bring in the B squad," Dinkins said. "You're going to bring in the A team, and you're going to bring in your best tunnelers, you're going to bring in your best engineer, and your best crew ... with one objective: You get the boss out."
One Mexican official estimated the tunnel took about a year to build, and that whoever built it took out about 350 truckloads worth of sand and dirt.
The passageway stretched for more than a mile and ended inside a half-built house. Crews started building the house in December 2014, then stopped a few months later, according to a farmer who lived nearby. The facade appeared to be finished around February or March, the farmer said, but workers kept moving dirt around the property for months -- until the day before Guzman's escape, when all of them were gone.
2016: Slipping out of sight
By early 2016, Mexican authorities had once again homed in on Guzman's trail. This time, they zeroed in on a simple white concrete compound in Los Mochis, a coastal city in Guzman's home state of Sinaloa.
Dramatic video shows troops raiding the home, guns blazing.
But they didn't catch Guzman there.
The Sinaloa cartel boss, authorities later discovered, had slipped into an escape hatch behind a mirror.
From there, he ran for about a half mile, popping up from a manhole cover in the middle of a street.
Police captured Guzman later that day. And since then, he's been behind bars.
But investigators who've followed Guzman's career say there's no doubt there are other hideaways out there -- and that the cartel boss could try to escape again.
"He is the tunnel king," Dinkins said.