They competed in Allsvenskan where they finished first, 2012–13 Svenska Cupen where they were knocked out in the group stage, Svenska Supercupen where they won the competition against IFK Göteborg and the 2013–14 UEFA Europa League where they were knocked out in the third qualifying round.

Malmö FF also participated in one competition in which the club continued playing in for the 2014 season, 2013–14 Svenska Cupen.

Malmö FF started the season with a home fixture against newcomers Halmstads BK on 1 April which ended in a 1–1 draw.

Malmö FF ended the season at home against Syrianska FC with a 3–1 win on 3 November.

This resulted in Malmö FF positioning themselves second in the league table after IFK Göteborg with the same number of points albeit with a lesser goal difference.

This was followed up by two home wins which saw Malmö FF advance up to second place in the league table behind Helsingborg.

Malmö FF followed up the break by losing at home against Djurgårdens IF who they had previously lost against in the away fixture earlier in the season.

The club went on to win three consecutive fixtures in which the away match against Helsingborgs IF was crucial as this put Malmö FF six points ahead of their rivals and kept the gap down to IFK Göteborg who was now their primary title contender.

The club then later had the opportunity to increase their lead to seven points in the away fixture against BK Häcken as IFK Göteborg had lost their match against Djurgårdens IF just moments before the start of the game at Rambergsvallen.

In the next fixture at home against IF Bromapojkarna the away side equalized Malmö FF's early lead and held the club to a draw until the 86th minute when Guillermo Molins scored the winning goal, Molins had also scored the first goal of the game.

Malmö FF qualified for the group stage of the 2012–13 Svenska Cupen in the 2012 season by beating Sandvikens IF after extra time in round 2 in August 2012.

The match which ended 2–0 in Malmö FF's favour was played on 10 March 2013 at Skytteholms IP in Solna.

The match was played at home at Swedbank Stadion on 10 November 2013 and the club's opponents was 2012–13 Svenska Cupen winners IFK Göteborg.

Malmö FF qualified for the 2013–14 UEFA Europa League by merit of finishing third in the 2012 Allsvenskan.

Malmö FF were drawn against Irish club Drogheda United in the first qualifying round.

The first leg of the match was played in Swansea on 1 August and ended in a 4–0 victory for the home side.

The second leg played in Malmö on 8 August ended in a goalless draw which confirmed the aggregate score to 4–0 in favour of Swansea City.

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