Koke was again an important member of Atlético's midfield in 2011–12, under both Gregorio Manzano and his successor Diego Simeone. He scored his first league goal of the campaign on 29 April 2012, opening the score in the 62nd minute of an eventual 2–2 away draw against Real Betis. He appeared in 13 matches during the club's successful Europa League run, including a 90th-minute substitute appearance in the 3–0 defeat of Athletic Bilbao in the final.