A comprehensive profile of flavonoids in bergamot juice was obtained by a single DAD-ESI-LC-MS-MS course. Eight flavonoids were found for the first time, five of these are C-glucosides (lucenin-2, stellarin-2, isovitexin, scoparin, and orientin 4'-methyl ether), and three are O-glycosides (rhoifolin 4'-O-glucoside, chrysoeriol 7-O-neohesperidoside-4'-O-glucoside, and chrysoeriol 7-O-neohesperidoside). A method is proposed to differentiate chrysoeriol and diosmetin derivatives, which are often indistinguishable by LC-MS-MS. In-depth knowledge of the flavonoid content is the starting point for bergamot juice exploitation in food industry applications.