Ahead of the 2015–16 season, Lindgren resumed his duty as FC Groningen’s captain following the departure of Maikel Kieftenbeld. He captained the club’s first two matches of the season, including a 2–0 loss against PSV Eindhoven in the Johan Cruyff Shield. However, Lindgren suffered ankle injury while training and missed three matches as a result. He didn’t make his return until on 2 September 2015 against VV Pelikaan-S in a friendly match, starting the whole game, in a 5–0 win. Since returning from injury, Lindgren was featured in the club’s four matches, as well as, retaining his captaincy. However, he suffered ankle injury once again and was sidelined for the rest of the year. Lindgren didn’t make his return from injury until on 8 January 2016 against Oostende in a friendly match, as FC Groningen won 1–0. Following his return, he resumed his first team place, playing in the centre–back position, as well as, his captaincy for the rest of the 2015–16 season. Lindgren then scored his first goal of the season, in a 1–0 win against ADO Den Haag on 3 April 2016, to end the club’s six matches without a win. This was followed up by scoring his second goal of the season, in a 3–1 win against De Graafschap. A month later on 8 May 2016, he scored twice against Heracles Almelo on the last game of the season, as FC Groningen won 2–1. Four days later on 12 May 2016 against Heracles Almelo in the first leg of the league’s semi-final play–off spot for the UEFA Europa League, Lindgren scored once again, as the club won 2–1, in what turns out to be his last appearance for FC Groningen. However, he missed the return leg due to a knee injury and because of his absent, the club lost 5–1 in the return leg, resulting FC Groningen missing out a place in the UEFA Europa League next season. At the end of the 2015–16 season, Lindgren went on to make twenty–four appearances and scoring five times in all competitions.