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At the start of the 2016–17 season, Minamino scored his first goal of the season, in a 3–1 win over Vorwärts Steyr in the first round of the Austrian Cup. After being away from the FC Red Bull Salzburg, due to international commitment, he scored on his return on 20 August 2016, in a 3–1 win over SV Mattersburg. Two weeks later on 11 September 2016, Minamino scored a brace, in a 4–0 win over FC Admira Wacker Mödling. He later scored three more goals, including another brace against Wolfsberger AC on 17 December 2016. Two months later on 19 February 2017, Minamino scored the first hat-trick of his Red Bull Salzburg career, in a 6–1 win over SV Ried. He played a huge role when he scored twice in a 5–0 win over FC Admira Wacker Mödling to reach the final of the Austrian Cup. Throughout the 2016–17 season, Minamino was featured in and out of the starting line-up, as he was mostly placed on the substitute bench. Despite this, he helped the side win both Austrian Cup and the league for the third consecutive time in his Red Bull Salzburg career. At the end of the 2016–17 season, Minamino went on to make 31 appearances and score 14 times in all competitions. During the season, he began to play in the striker position.