Scheffer often painted subjects from literature, especially the works of Byron and Goethe. His popular Faust-themed paintings include "Margaret at her Wheel"; "Faust Doubting"; "Margaret at the Sabbat"; "Margaret Leaving Church"; "The Garden Walk", and "Margaret at the Well". In 1836, he painted two pictures of Goethe's character "Mignon," and around the same time painted the acclaimed "Francesca da Rimini".
He now turned to religious subjects: "Christus Consolator" (1836) was followed by "Christus Remunerator", "The Shepherds Led by the Star" (1837), "The Magi Laying Down their Crowns", "Christ in the Garden of Olives", "Christ bearing his Cross", "Christ Interred" (1845), and "St Augustine and Monica" (1846).
Scheffer was also an accomplished portrait painter. His subjects included composers Frédéric Chopin and Franz Liszt, the Marquis de la Fayette, Pierre-Jean de Béranger, Alphonse de Lamartine, and Queen Marie Amélie.
After 1846, he ceased to exhibit. His strong ties with the royal family caused him to fall out of favour when, in 1848, the Second Republic came into being. Shut up in his studio, he produced many paintings that were only exhibited after his death, which took place at Argenteuil on the 15th of June 1858. He is buried in the Cimetière de Montmartre.
Works first exhibited posthumously include "Sorrows of the Earth", and the "Angel Announcing the Resurrection", which he had left unfinished. By the time of his death, his reputation was damaged: though his paintings were praised for their charm and facility, they were condemned for poor use of color and vapid sentiment.
Scheffer was married to the widow of General Baudrand. His brother Henry, born at the Hague on September 27, 1798, was also a prolific painter. Scheffer was made commander of the Legion of Honour in 1848, that is, after he had wholly withdrawn from the Salon.