Despite struggling to regain his fitness ahead of the 2016–17 season, Compper managed to regain his first team place in central defence at the start of the season. He appeared in every match for the side since the start of the season. However, in November 2016, Compper suffered a tear in a joint capsule that kept him out for the whole year. Compper then scored on his return from injury on 21 January 2017, in a 3–0 win over Eintracht Frankfurt. Since returning from injury, Compper continued to regain his first team place towards the end of the season and helped the side finish in the second place to qualify for the UEFA Champions League next season. Despite being sidelined on three occasions later in the 2016–17 season, he went on to make a total of 26 appearances and scoring twice in all competitions. At the end of the 2016–17 season, Compper signed a contract extension until 2019.