Krychowiak made his third debut for the club as a starter in a 1–0 loss against Marseille in the opening game of the season. Since joining Stade Reims on a permanent basis, he quickly established himself in the starting eleven, playing in the defensive midfield position. His performance against AS Nancy on 20 September 2012 drew comparison to Zlatan Ibrahimović after he set up one of the club's two goals in the game, with a 2–0 win. On 26 January 2013, Krychowiak scored his first goal for Reims in a 1–1 draw against Toulouse. He later scored three more goals, all of which were winning goals against Paris Saint-Germain, Lyon and Lorient. Despite missing three matches throughout the 2012–13 season, Krychowiak went on to make 36 appearances and scoring four times in all competitions.