On his return to Europe in 1820 Martius was appointed as the keeper of the botanic garden at Munich, including the herbarium at the Munich Botanical Collection, and in 1826 as professor of botany in the university there, and he held both offices until 1864. He devoted his chief attention to the flora of Brazil, and in addition to numerous short papers he published the "Nova Genera et Species Plantarum Brasiliensium" (1823–1832, 3 vols.) and "Icones selectae Plantarum Cryptogamicarum Brasiliensium" (1827), both works being finely illustrated. An account of his travels in Brazil appeared in three volumes between 1823 and 1831, with an atlas of plates, but probably the work by which he is best known is his "Historia naturalis palmarum" (1823–1850) in three large folio volumes, in which all known genera of the palm family are described and illustrated. The work contains more than 240 chromolithographs, with habitat sketches and botanical dissections. In 1840 he began the "Flora Brasiliensis", with the assistance of the most distinguished European botanists, who undertook monographs of the various orders. Its publication was continued after his death under the editorship of A. W. Eichler (1839–1887) until 1887, and subsequently of Ignatz Urban. He also edited several works on the zoological collections made in Brazil by Spix, after the death of the latter in 1826. In 1837, he was elected a foreign member of the Royal Swedish Academy of Sciences.