Formentera returned to the fourth division in 2012, after winning the regional Preferente. In 2015–16, they reached the second round of the cup with a 2–1 win at Segunda División B team CD Alcoyano,[6] and a year later they reached the last 32 of the competition before a 14–2 aggregate loss to La Liga team and UEFA Europa League holders Sevilla FC.[7]
In that 2016–17 season, Formentera promoted for the first time ever to the third division after defeating Alavés B in the promotion play-offs.[8] The following season, they reached again the round of 32 of the Copa del Rey, where they eliminated top level club Athletic Bilbao after winning in San Mamés with a goal in the sixth minute of stoppage time;[9] in the last 16 they were eliminated by another top-flight Basque team, Deportivo Alavés,[10] and the league season ended with instant relegation.[11]