The house in Los Mochis, a northwestern seaside city in Guzman's native Sinaloa state, bears the scars of Friday's fierce pre-dawn gunfight, with dried blood on the floors.
A video released by the government shows the marines firing their assault rifles and tossing smoke grenades before entering the rooms.
One troop was wounded and was on the ground. "Stay calm, buddy," one marine told him.
As they moved inside, they arrested one man. They screamed at a woman who was hiding in a bathroom, asking her where the kingpin was. "I don't know, sir," she answered.
When the dust settled, five gunmen were dead, one marine wounded and six suspects detained.
The 58-year-old kingpin, meanwhile, was nowhere to be seen. His security chief, Orso Ivan Gastelum, was also missing.
Dvds And Lingerie
The marines frantically searched the house.
In one bedroom, three DVDs of the TV series "La Reina del Sur" were on a bed. The star of the show about a drug queen is Kate del Castillo, the Mexican actress who brokered the notorious October meeting between Guzman and US actor Sean Penn.
The authorities found out about the clandestine meeting and nearly caught Guzman in early October. They eventually tracked him down in Los Mochis, where he arrived on the eve of the raid.
The shrapnel from stun grenades was still in the main room when reporters were allowed to tour the house on Monday. Food was rotting in the kitchen. Authorities said food had been ordered for 13 people on the eve of the raid.
Dried blood stains were splattered in the entrance and another room of the white house.
On the second floor, there were three bedrooms, including one with evidence that a woman slept there, including lace lingerie, makeup and a hairdryer on the ground.
The top floor had a patio with more bullet holes. "Guzman's gunmen tried to flee through here," an official from the attorney general's office said.
Suspecting that Guzman had fitted the home with a tunnel, the soldiers scoured the house. They moved the refrigerator, which had bullet holes, but no tunnel was there.
"Since we know that his modus operandi is tunnels, the soldiers moved the fridge to see if there was one back there," the official said.
Their suspicions were justified since he used a 1.5 kilometer (one-mile) tunnel to secretly flee prison in July. Meanwhile, he had an escape hatch into drainage systems in his home in another Sinaloa city.
In Los Mochis, the drug lord's last underground escape route was in a bedroom where the bed's mattress was nearly on the ground and men's clothing was strewn about the floor.
Inside the closet, a mirror opened into the tunnel. The wall was covered with bullet impacts.
Metal steps led down to the subterranean passage, which was about two meters (6.6 feet) high and one meter (3.3 feet) wide with concrete walls and lights.
The floor was covered with belt-high water, while a dead snake was spotted.
The 20-meter long passage leads to a steel hatch door, which officials said opens to the city's storm drain system.
Guzman and Gastelum fled through the drainage network for about one kilometer (half a mile) until they finally popped out of a manhole.
They stole a car but were finally intercepted by the marines, flown to Mexico City and taken to the same maximum-security prison that Guzman escaped from six months ago, from which he now faces extradition to the United States.