Zenoni started his career at his native club Atalanta B.C., joining the team's youth system in 1994. After being promoted to the first team, in 1996, Zenoni was loaned to Serie C1 side A.C. Pistoiese for a season in order to gain playing time and experience. The following season, he made his Serie A debut with Atalanta on 5 October 1997, in a 1–1 draw against rivals Brescia; in total he made 17 appearances throughout the season. Despite his promising performances for the club, he was unable to help Atalanta avoid relegation to Serie B. He later helped Atalanta gain promotion to Serie A during the 1999–2000 season, and the next season, both he and his brother Damiano established themselves as two of the most exciting young full-backs in the league. Described by press as a promising young prospect, in June 2001, Cristian transferred to A.C. Milan along with Massimo Donati for 60 billion Italian lire in a cash plus player deal (the player was majority), but quickly transferred to Juventus F.C. as part of Filippo Inzaghi's transfer in the opposite direction, he was tagged for 30 billion Italian lire or about €15.6M. He signed a 5-year contract. In the summer of 2003, Zenoni was loaned to U.C. Sampdoria with an option to sign permanently for 10 million euro. He was loaned out to the club once again in the summer of 2004, and at the end of the 2004–05 season, after almost helping the team qualify for the UEFA Champions League, he was signed permanently by Sampodoria for €1M. After several seasons in Genoa, in 2008, Zenoni joined Bologna. In 2010, he moved to AlbinoLeffe, where he remained until 2011. He ended his career after spending the 2011–12 season with Monza, in Lega Pro. In total, he made 546 professional appearances, scoring 10 goals.