Colantuono's Serie C1 coaching debut, in 2002–03, ended in another fifth place, securing a place in the promotion playoff, then lost to Pescara. In the meanwhile, Luciano Gaucci, owner of Sambenedettese, Serie B team Catania and Serie A team Perugia at the time, appointed Colantuono at the helm of the Sicilian side. Colantuono, again supported by Matricciani because of his lack of a regular coaching license, led Catania to a fairly good season in ninth place. In 2004–05, after Catania was sold by the Gaucci family, Colantuono, finally authorized to act as first team coach, signed for Perugia, just relegated to Serie B. He led the team to a spot in the promotion playoff, then lost to Torino. After the cancellation of Perugia, in 2005–06 Colantuono accepted the offer of Atalanta, leading the "nerazzurri" to a clear Serie B win. In the 2006–07 season, he led Atalanta to an eighth-place finish in the Serie A table.