Born in Milan, Bonfanti joined the academy of Atalanta in 2015, aged 12,[1][2] and subsequently came through the club's youth ranks;[2][3] in the summer of 2021, he was sent on loan to Sampdoria,[1][4][5] where he played for the under-19 squad, while receiving his first call-ups to the first team, under head coach Marco Giampaolo.
[6][7] The defender made a total amount of 23 appearances (split between the league and the Coppa Italia Serie C) for the club throughout his first professional season.
[3][8] Having returned to Atalanta in the summer of 2023, Bonfanti started training with the first team during the pre-season, under manager Gian Piero Gasperini;[1][8][9] at the start of the league campaign, he was initially assigned to the club's newly-formed reserve team, Atalanta Under-23.
[10] After establishing himself as a regular starter for the reserve team,[2][8] the defender made his Serie A debut on 25 November, coming on as a substitute for Sead Kolašinac in the 76th minute of a 2–1 league defeat to Napoli.
[2][11] On 14 December, he made his debut in a European competition, starting and scoring his first professional goal in a 4–0 UEFA Europa League win over Raków Częstochowa in the group stage.