On 27 January 2015 Swedish champions Malmö FF announced that they had signed Yotún on a three-year contract. He arrived in Malmö as a left back, where he played for the 2015 season. After becoming the third choice left back behind newly arrived Behrang Safari and Pa Konate during the 2016 season, Yotún was played at various midfield positions, where he excelled. Yotún emerged as a key player during the first half of the 2017 season, and was voted Malmö FF player of the month by the supporters in July.