The Prince and the Pauper (1881) by Mark Twain. The novel includes a depiction of Mary before her accession: "When his royal 'sister,' the grimly holy Lady Mary, set herself to reason with him against the wisdom of his course in pardoning so many people who would otherwise be jailed, or hanged, or burned (...) the boy was filled with generous indignation, and commanded her to go to her closet, and beseech God to take away the stone that was in her breast, and give her a human heart." The short appearance had a considerable influence on her negative image, given the enduring popularity of Twain's work. His depiction of her as a cold and cruel person seems to be connected both to Twain's outspoken atheism and to the strong anti-Catholic prejudice prevalent in American society at the time of writing.
Young Bess (1944), Elizabeth, Captive Princess (1948), and Elizabeth and the Prince of Spain (1953) by Margaret Irwin. A trilogy focusing on the early years of Elizabeth I of England and her relationship with Mary and Philip II of Spain.