Malmö FF also participated in one competition in which the club continued playing in for the 2013 season, 2012–13 Svenska Cupen.

Due to these circumstances third captain Jiloan Hamad held the captaincy for the majority of the matches throughout the season.

The competitive league season started on 2 April when Malmö FF played against Gefle IF in a home fixture at Swedbank Stadion, the match ended in a draw 0–0.

However, the team lost surprisingly away from home against the relegation threatened Örebro SK who had only won one match before this.

The last home game of the season at Swedbank Stadion against already relegated Örebro resulted in a 1–1 draw, Malmö now positioned second had to win their last game against AIK at the same time as Elfsborg lost points at home against Åtvidabergs FF.

Malmö dropped down to a final third place as Häcken won their last game of the season away from home against Sundsvall 2–1.

Mathias Ranégie became Malmö FF's best goalscorer of the season with 6 goals scored even though he was sold to Italian side Udinese on the last day of the summer transfer window.

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