In 1808, at the age of twelve, he entered the École nationale supérieure des beaux-arts de Lyon, where he studied with Pierre Revoil and Alexis Grognard (1752-1840).
Shortly after, Guérin was named Director of the Villa Medici and Bonnefond accompanied him to Rome.
While in Italy, he also visited Campania and Tuscany and made the acquaintance of several German painters of the Nazarene movement, including Julius Schnorr von Carolsfeld, Joseph Anton Koch and Johann Friedrich Overbeck.
In 1830, Victor Prunelle, the Mayor of Lyon, offered him the directorship of the École des Beaux-arts.
He created a school of engraving, operated by Victor Vibert (1799-1860), and the École produced seventeen laureates of the Prix de Rome between 1831 and 1860.