By 1589, Lodge had turned his attention to long poems and fictions, publishing such works as Scillas Metamorphosis (1589); Rosalynde: Euphue Golden Legacie (1590), which Shakespeare famously drew on for As You Like It; The Famous, True and Historicall Life of Robert, Second Duke of Normandy (1591); Euphues Shadow (1592); The Life and Death of William Longbeard (1593); and A Margarite of America (1596), which Lodge claimed to have written on a sea voyage to South America. In his later works, Lodge mined the moral-philosophical vein and at times explicitly demonstrated his Catholicism. Lodge’s last collection of poetry, A Fig for Momus (1596), included epistles, satires, and eclogues in a conscious alignment with such Roman satirists as Horace and Juvenal. Lodge’s late poems are sometimes read as precursors in both style and form to the Augustan age poets.
Lodge left England in 1597 to earn a medical degree from the University of Avignon. Returning to England, he practiced medicine, married, and began work on translations of the Jewish historian Josephus and the Roman writer Seneca. Lodge also continued to publish shorter works, including a translation of Catholic devotional verses, A Treatise of the Plague (1603), translations, and works of popular medical knowledge. He practiced medicine, presumably until his death, caused by plague.