His many portraits show the influence of Velázquez, Jusepe de Ribera and other Spanish masters, as well as Titian and Van Dyke, whose works he studied in the Prado, which placed him at the forefront of painting in France in the 1850s, opposing neoclassicism and academicism.

Following the period in Spain, Bonnat worked the studios of the history painters Paul Delaroche and Leon Cogniet (1854) in Paris.

During his stay in Rome, he also became friends with Edgar Degas, Gustave Moreau, Jean-Jacques Henner and the sculptor Henri Chapu.

Julius Kaplan characterised Bonnat as "a liberal teacher who stressed simplicity in art above high academic finish, as well as overall effect rather than detail.

"[2] Bonnat's emphasis on overall effect on the one hand, and rigorous drawing on the other, put him in a middle position with respect to the Impressionists and academic painters like his friend Jean-Léon Gérôme.

Gautier hailed him as "the antithesis of Bouguereau," because of the stark naturalism and lack of surface finish that characterize Bonnat's work.

Some of Bonnat's more notable students include: John Singer Sargent, Stanhope Forbes, Gustave Caillebotte, Prince Eugen, Duke of Närke, Gustaf Cederström, Laurits Tuxen, P. S. Krøyer, Suzor-Coté, Robert Harris, Alfred Philippe Roll, Georges Braque, Thomas Eakins, Raoul Dufy, Jean Béraud, Franklin Brownell, Marius Vasselon, Hubert-Denis Etcheverry, Fred Barnard, Louis Béroud, Paul de la Boulaye, Aloysius O'Kelly, Erik Werenskiold, Graciano Mendilaharzu, Edvard Munch, Alphonse Osbert, Henry Siddons Mowbray, Francis Petrus Paulus, Charles Sprague Pearce, Henri de Toulouse-Lautrec, Manuel Cusí y Ferret, Hyakutake Kaneyuki, Nils Forsberg, Walter Tyndale, Émile-Louis Foubert, and Harry Watrous.

It includes an exceptionally fine collection of Old Master drawings from Leonardo da Vinci and Michelangelo to Ingres and Géricault.