Mirante was signed by Bologna on a free transfer on 3 July 2015. He was the first choice of the team. On 19 July 2016, Mirante signed a new three-year contract. However, at the start of 2016–17 season he was diagnosed with a heart problem and had to undergo testing which ruled him out indefinitely; on 31 August 2016 the club signed Alfred Gomis on loan from Torino as an emergency replacement. After missing the next two and a half months of the season, he was finally cleared to play in mid November. Mirante made his debut since his injury on 28 November 2016 against Atalanta. He was the captain of Bologna in 2017–18 season, his last season with the club.