Damiano Zenoni began his career with the Atalanta youth side, and was later promoted to the club's senior side. He was initially sent on loan to Pistoiese and Alzano Virescit for the 1996–97 and 1997–98 seasons in order to gain experience and playing time. After helping Atalanta back to the top Italian division, Zenoni made his Serie A debut with Atalanta on 1 October 2000, against S.S. Lazio, and along with his brother, Cristian, established himself as one of the most promising young full-backs in the league throughout the 2000–01 season.