He was born in Bayonne, but from 1846 to 1853 he lived in Madrid, Spain, where his father owned a bookshop. Thus, Léon Bonnat began his formal artistic training at the Royal Academy of Art in Madrid. His primary master was the leading artist in Spain, Federico de Madrazo, and Bonnat was one of the few foreign artists of the nineteenth century to study Spanish art as part of an official curriculum. After the death of his father in 1853, Bonnat and his family moved to Paris, where he entered the École des Beaux-Arts in 1854 and the independent atelier run by Cogniet. During these years, Bonnat received annual scholarships from the municipal council of his hometown of Bayonne, and when he won only a second prize in the Prix de Rome of 1857, Bayonne again provided the funding for him to go to Rome to complete his artistic education from 1858 to 1861.
Bonnat had already begun exhibiting at the Salons in 1857 and continued, with increasing success, during the 1860s. His painting style in this period generally featured powerful, naturalistic forms, often illuminated in dramatic chiaroscuro and modeled in fairly broad, thick paints of a rather limited palette.
During the 1860s, the French government, the cities of Paris and Bayonne, the French emperor and empress, art dealers, and private individuals all purchased or commissioned works of art from Bonnat in a variety of genres: history, religious, mythological, allegorical, portrait, and genre painting.
By 1867 Bonnat was named to the Legion of Honor, and in 1869 he won the gold medal at the Salon. With the 1870s he became internationally esteemed as a portraitist and could demand extremely high prices for these works. He modified his mode into a more intense realism with even stronger light-dark contrasts. His many portraits show the influence of the Spanish Old Masters, especially Ribera and Velázquez, as well as Titian and Van Dyck, whose works he studied in the Prado.
Bonnat's vivid portrait-painting is his most characteristic work, but his history paintings, such as the "Martyrdom of St Denis in the Pantheon", are also famous. Bonnat was one of Edouard Manet's friends -- both shared a love of Spanish painting, and he worked with Puvis de Chavannes. His financial success enabled him to indulge his great passion for collecting art, and by the 1890s he had acquired objects of great value, particularly drawings. In 1890 Bonnat initiated a project to build a museum in Bayonne and bequeath his art collections to it, a plan that was finally realized with the opening of the Musée Bonnat in 1902
Bonnat was quite popular with American students in Paris. He spoke several languages and knew English well. In May 1905 he succeeded Paul Dubois as director of the Ecole des Beaux-Arts. Léon Bonnat was a liberal teacher who stressed simplicity in art above high academic finish, as well as overall effect rather than detail.