The couple separated in April, according to the divorce petition, the Louisville Courier-Journal reported, and Schnatter's wife, Annette Cox, recently bought a house.
In a 2013 interview, Schnatter, 57, said that Cox, 59, was "the finest human being" he'd ever met.
His net worth is estimated at about $500 million after the company's stock declined and he sold off some of his shares, the Courier-Journal reported.
The couple owns several homes, including a $23 million condo in Deer Valley, Utah, an $11 million home in Louisville, Ky., and a $6 million condo in Naples, Fla.
Schnatter founded Papa John's in 1984 and became the face of the brand through a series of TV commercials, often featuring former NFL quarterback Peyton Manning.
He was forced to resign as CEO and board chairman of the company in 2018 after he used the n-word during a conference call while defending support from white nationalist groups over his criticism of national anthem protests at NFL games, Forbes reported.
Meanwhile, Schnatter filed a lawsuit Thursday claiming an advertising firm tried to extort him for $6 million and then leaked the n-word audio to Forbes when the money wasn’t paid, the Courier-Journal reported.
He has also expressed dismay with Papa John's since his departure, claiming the pizzas no longer taste the same. Rob Lynch, the company’s current CEO, said they haven’t made any changes to the recipe.
Schnattner and his wife have two grown children.