Having been placed on the substitute bench at the start of the 2016 season, Konate made his first appearance of the season against IF Elfsborg on 18 April 2016, starting the whole game, and helped Malmö FF kept a clean sheet, in a 1–0 win. This was followed up by helping the club kept three more consecutive clean sheets against Djurgårdens IF, IFK Göteborg and BK Häcken. However in Svenska Cupen Final against BK Häcken, he started the whole game, as the club lost 6–5 in a penalty shoot–out following a 2–2 draw. Since returning to the first team, Konate regained his first team place, playing in the left–back position for the next two months. This last until he was called up to the Sweden Olympic squad for the Summer Olympics. After the tournament ended, Konate made his return to the first team, coming on as a 58th-minute substitute, in a 4–1 win against Jönköping Södra on 22 August 2016. Following his return, however, he lost his first team place by new signing, Behrang Safari and found his playing time, mostly coming from the substitute bench. Despite this, Konate's contributions saw Malmö FF win the league once again after the club beat Falkenbergs 3–0 on 26 October 2016. He later reflected on the season, saying: "I have had a good season and received much more matches and more confidence from Allan Kuhn. I did well when I got the chance. Then it is clear that you want to play all matches, but that is in football. It has been a good season." At the end of the 2016 season, Konate went on to make twenty–four appearances in all competitions.