The career criminal with the nickname “Killa” who was sitting behind the wheel when NYPD Officer Jonathan Diller was gunned down during a traffic stop Monday evening has been charged after police discovered a second gun in the car.

Lindy Jones, 41, was charged Wednesday morning with criminal possession of a weapon and defacing a weapon.

Jones was in the driver’s seat of a double-parked Kia Soul outside a T-Mobile store in Flatbush when NYPD “quality of life” officers, including Diller, conducted the stop.

The man in the passenger seat, 34-year-old Guy Rivera, refused the cops’ request to exit the car before allegedly whipping out a gun and shooting Diller, a husband and father to a 1-year-old son, in the stomach.

Shortly before Jones was charged, officers recovered a second weapon, a 9-millimeter firearm, in the glove compartment of the vehicle, sources told The Post.

They are now investigating if the gun belongs to Jones.

Rivera, who was injured when Diller’s partner returned fire Monday night, is still recovering at the hospital. He has not yet been charged.