At the start of the 2012–13 season, Matmour was placed on the substitute bench for the first three matches of the season following a thigh injury he sustained. By September, Matmour soon received a handful of playing time, mostly coming from the substitute bench. He then scored his first goal (and only) of the season, in a 3–1 win over Hannover 96 on 20 October 2012. Despite his goal drought, his performance convinced Manager Armin Veh, saying: "Karim deserves to play from the start." The following month saw the player was sent–off on two occasions, both of them were second bookable offence against Schalke 04 and Fortuna Düsseldorf. Following his return, Matmour continued to find his playing time, coming from the substitute bench for the rest of the 2012–13 season. His contributions helped the club finished sixth place in the league, resulting in Eintracht Frankfurt’s qualification in the UEFA Europa League next season. At the end of the 2012–13 season, he went on to make 24 appearances and scoring once in all competitions.