Bugno's performance in the Grand Tours, however, was over-shadowed by Miguel Indurain. Bugno's victory in the Giro d'Italia in 1990 is considered one of the most dominant performances in that race — he led from start to finish. While he won the Giro in 1990, he finished second to Indurain in the Tour de France in 1991 and third behind Indurain and Claudio Chiappucci in 1992. In a battle in the 1992 Tour, Indurain kept his calm despite Chiappucci's attack in the Alps; Bugno had to chase and cracked in the final parts of the stage. Indurain was quoted as saying that Bugno was his biggest threat in the Tour.
Bugno retired following the 1998 road season and is now a helicopter rescue pilot. He piloted a camera helicopter for the Tour of Lombardy, on 20 October 2007, and for the whole of the 2008 Giro d'Italia. He ran for a seat in Lombard Regional Council in the Lombard regional election, 2010 for the centre left coalition of political parties but he was not elected.
He has remained involved with the Giro d'Italia by being one of the TV helicopter pilots for the Italian national broadcaster, RAI.
He is the president of CPA (Association of Professional Cyclists). In November 2012, in the wake of the Lance Armstrong doping scandal, he demanded that an independent anti-doping body be established. He stated that the UCI could not be trusted to enforce the rules.