At the start of the 2012–13 season, Samba helped the club kept six clean sheets and progress to the UEFA Europa League Group Stage after beating the teams of Budapest Honvéd, Vitesse and AZ Alkmaar. He also started the season as well in the league, assisting two goals in the first two league matches against Kuban Krasnodar and FC Rostov. It wasn’t until on 2 September 2012 when he scored his first goal of the season, in a 2–1 loss against Krylia Sovetov Samara. Samba continued to regain his first team place, playing in the centre–back position. Two months later on 4 November 2012, he scored his second goal of the season, in a 3–1 win against Terek Grozny. Three weeks later on 22 November 2012, Samba scored his third goal of the season, in a 2–0 win against Udinese to qualify for the UEFA Europa League Knockout Stage. However, during the match, he received a heavy blow to the head and was sideined as a result. It wasn’t until on 2 December 2012 when Samba returned to the starting line–up and helped the side win 2–0 against CSKA Moscow. By the time he departed Anzhi Makhachkala in January, Samba went on to make twenty–nine appearances and scoring three times in all competitions.