The anti-virus guru was detained at a hotel in an upscale Guatemala City neighborhood with the help of Interpol agents and taken to an old, three-story building used to house migrants who enter the country illegally, said Interior Minister Mauricio Lopez Bonilla.
It was the latest twist in a bizarre tale that has seen McAfee refuse to turn himself in to authorities in Belize, where he is a person of interest in the killing of a neighbor, then go on the lam, updating his progress on a blog and claiming to be hiding in plain sight, before secretly crossing the border into Guatemala.
Earlier Wednesday, McAfee said he had formally requested asylum in Guatemala after entering the country from Belize, where he says he fears for his safety because he has sensitive information about official corruption and refused to donate to local politicians.
"Yes, we are presenting this, and I want it to be clear, because of the persecution, not because of the murder," he told the AP about his asylum bid.
Police in Belize deny they are persecuting McAfee and say there is no warrant for his arrest. The country's prime minister has even questioned McAfee's mental state. Since there are no restrictions on his travels, it's unclear why McAfee would need any special status in order to stay in Guatemala.
The 67-year-old went on the run last month after officials tried to question him about the killing of Gregory Viant Faull, who was shot to death in early November on the Belize island where both men lived.
McAfee had engaged in a series of clashes with neighbors and authorities over allegations he kept aggressive dogs, illegal weapons and drug paraphernalia in his beachfront home on a Belize island. McAfee acknowledges that his dogs were bothersome and that Faull had complained about them, but denies killing Faull.
Faull's home was a couple of houses down from McAfee's compound.
The Faull family has said through a representative that the murder of their loved one on Ambergris Caye has gotten lost in the media frenzy provoked by McAfee's manipulation of the press through phone calls, emails and blog posts detailing his life on the lam.
McAfee dropped out of sight after police said they were seeking him, although he grabbed global attention with regular phone calls with reporters and blog updates. He claimed to be wearing disguises and watching as police raided his house. It was unclear, however, how much of what McAfee - a confessed practical joker - said and wrote was true.
At one point, he even posted on his blog that he mounted an elaborate ruse in Mexico to cover his flight.
"My 'double,' carrying on (sic) a North Korean passport under my name, was detained in Mexico for pre-planned misbehavior," McAfee wrote in the posting, "but due to indifference on the part of authorities (he) was evicted from the jail and was unable to serve his intended purpose in our exit plan."
McAfee hasn't provided details on how he crossed from Belize into Guatemala.
He had earlier said he didn't plan to leave Belize but ultimately did because he thought "Sam" was in danger, referring to the young woman who has accompanied him since he went into hiding.
McAfee, the creator of the McAfee antivirus program, has led an eccentric life since he sold his stake in the anti-virus software company that is named after him in the early 1990s and moved to Belize about three years ago to lower his taxes.
He told The New York Times in 2009 that he had lost all but $4 million of his $100 million fortune in the U.S. financial crisis. However, a story on the Gizmodo website quoted him as calling that claim "not very accurate at all." He has dabbled in yoga, ultra-light aircraft and producing herbal medications.