A year later, Victor Meirelles, wanting to retire, offered Júnior his position as professor of history painting at the Imperial Academy of Fine Arts, but Júnior refused the offer because he preferred to stay in São Paulo. From 1887 to 1896, he made three more trips to Europe. He increasingly rejected Biblical and historical subjects in favor of regionalist themes, depicting the everyday life of the caipiras while moving from academic style to Naturalism. Despite these changes, his reputation at the Imperial Academy remained unchallenged, and he received its Gold Medal in 1898.
In front of the Hotel Central in Piracicaba, Júnior was stabbed to death in 1898 by his cousin José de Almeida Sampaio. Júnior had been having a long-standing affair with Sampaio's wife, Maria Laura do Amaral Gurgel, who had briefly been engaged to Júnior, and Sampaio had just found out about it.