Colantuono led Atalanta's successful return to the top flight during the 2011–12 Serie A season, resulting in a comfortable 12th-place finish, despite the club beginning the season with a six-point deduction for its involvement in the 2011–12 Italian football scandal. An additional deduction of 2 points followed before the 2012–13 Serie A season; however, Colantuono still managed to guide Atalanta to safety with a 15th-place finish. Keeping with their manager for the 2013–14 Serie A campaign, Coulantuono secured 11th place and some impressive performances, including victories of local rivals Internazionale and A.C. Milan. Before the start of the 2014–15 Serie A season, Coulantuono committed his future to Atalanta, however, the season did not go well and after a poor run of form he was dismissed on 4 March 2015 and replaced by Edy Reja, leaving Atalanta only 3 points above the relegation zone. He took up the head coach position soon after at Udinese.