The company announced the move Tuesday. Manning is still tied to the company through an agreement, and will serve as a spokesman and brand ambassador.
"After six successful and rewarding years, Peyton Manning and Papa John's International have sold their stake in 31 Papa John's locations, which were part of a joint-venture in the Denver, Colo., market," the company said in a statement. "Peyton remains an official Papa John's spokesperson and brand ambassador as part of his long-term agreement with the brand."
Manning first bought 21 stores in 2012.
"It's a smart investment now and will be long after I'm done playing football," Manning said in a 2012 news release. "I'm particularly impressed by John's drive to make everything about Papa John's better along with his ambition and plan to continue growing the brand around the world. Also, Papa John's being the Official Pizza of the Denver Broncos makes this even more exciting."
The five-time NFL MVP and two-time Super Bowl champion retired following the 2015 season after making more than $400 million in career earnings, according to Forbes. The No. 1 overall pick in the 1998 NFL Draft spent his first 13 seasons with the Indianapolis Colts before signing with the Denver Broncos during the 2012 offseason.
Manning owns the NFL records for career passing yards, touchdowns, sack percentage, comebacks and total offense.
Papa John's signed a multi-year sponsorship deal with the NFL in 2010. The company's latest contract with the league "mutually" ended on Feb. 28, a day before the NFL agreed to a new deal with Pizza Hut.
Papa John's founder and CEO John Schnatter stepped down from his role with the company in December after saying the NFL's handling of national anthem protests hurt pizza sales. He later apologized for his remarks.
Schnatter remains a Papa John's chairman and his face still appears on the company's pizza boxes.
"The NFL has hurt us," Schnatter said in a November conference call. "We are disappointed the NFL and its leadership did not resolve this."
Schnatter's replacement, Steve Ritchie, said the company still has team partnerships with more than 20 NFL franchises.
The company said the new owner of Manning's Denver locations plans to rehire all existing employees.
Papa John's said in a news release that its fourth-quarter sales were down by nearly 4 percent in 2017, compared to 2016 sales for that same time period.