Freuler made 29 starts in the 2016–17 season, in which Atalanta finished fourth in the table, a nine place improvement under first-year manager Gian Piero Gasperini. Atalanta also qualified for the group stages of the Europa League for the first time since 1990. Freuler found his name on the scoresheet five times, and also provided four assists. On 28 April, Freuler scored a late equaliser at home to eventual champions Juventus, derailing their chance to clinch the "Scudetto" that weekend.