At the time his team attributed his loss to a "psychological crisis" and Cunego said "a great weight has been lifted from me by this defeat."

In the Tour de France Cunego was the winner of the young rider classification; he finished 2nd on stage 15 to Alpe d'Huez, after losing to Fränk Schleck, who broke away in the final 2 kilometres (1.2 miles).

In July 2013, he was one of 27 former riders and officials linked to the Lampre–Merida team indicted for doping in an Italian court, with a hearing set for 10 December 2013.

[9] In early 2014 however, details emerged that indicated that Cunego might have been one of few Lampre riders to refuse treatment by Spanish doctor José Ibarguren Taus, who was linked to doping practices.

He was quoted as saying that believes that the increased media attention and sponsor obligations interfered with his training and mental focus, ultimately preventing him from achieving his full potential after his 2004 Giro victory and other initial successes.

He also expressed concern about the state of 2020s Italian cycling, highlighting the lack of emerging talent compared to other nations.