On 11 August 2015, he started the season for Sevilla in the 2015 UEFA Super Cup 5–4 loss against Barcelona, and suffered a broken rib but still played the full 120 minutes. Having started in the centre-back position in the opening game of the season, he continued to play in the defensive midfield position. As a result, the club began talks with Krychowiak over a new contract. Manager Unai Emery praised his performance, calling "his sacrifice and dedication towards the team always puts them at their service". On 5 November 2015, Krychowiak signed a contract extension with Sevilla, keeping him at the club until 2019. Shortly after, he captained the club in a number of matches for the rest of the year. After serving a one match suspension, he then scored his first goal of the season, in a 2–0 win against rivals Real Betis in the first leg of the Copa del Rey last 16 tournament. Three days later, on 9 January 2016, he suffered a knee injury that saw him sidelined for two months. On 20 March 2016, Krychowiak returned to the starting line-up against Real Madrid, as the club lost 3–2. Since returning to the first team, he later contributed two assists in two second leg matches in the UEFA Europa League quarter-final and semi-finals against Athletic Bilbao and Shakhtar Donetsk respectively, to send Sevilla to the UEFA Europa League Final for the third time in a row. He started in the UEFA Europa League Final against Liverpool and played the whole game as they won 3–1, winning the tournament for the third time in a row.