Professor Stein is an authority on European, Spanish, and colonial Latin American music of the late Renaissance and baroque eras, with particular emphasis on theater music and opera. Before coming to Michigan, she taught at the University of North Carolina at Chapel Hill and at The University of Chicago. In 1998 she was an invited professor at the Universidad Complutense in Madrid. She has received fellowships from Fulbright-Hayes, the American Council of Learned Societies, the National Endowment for the Humanities, the Delmas Foundation, and the Committee for Cultural Cooperation between the United States and Spain.

She has published essays, articles, and book chapters internationally, and has given lectures and seminars in Europe and Latin America, as well as in the U.S., and for the American Musicological Society, the Modern Language Association, the Royal Musical Association, and the International Musicological Society. Her first book, Songs of Mortals, Dialogues of the Gods: Music and Theatre in Seventeenth-Century Spain (Oxford University Press, 1993), was awarded a publication subvention from the American Musicological Society, as well as the 1995 First Book Prize from the Society for Spanish and Portuguese Historical Studies. Her second book is an expanded second edition of Howard Mayer Brown, Music in the Renaissance (Prentice-Hall, 1998). Her performing edition of the first opera performed in the Americas, La púrpura de la rosa (Lima, 1701), by Tomás de Torrejón y Velasco and Juan Hidalgo, was published in Madrid in 1999 and used for the BMG Classics recording directed by Andrew Lawrence-King, for which she also served as artistic advisor and dramaturg.

In 1996 the American Musicological Society recognized her with the Noah Greenberg Award for "distinguished contribution to the study and performance of early music." She has collaborated regularly with Jordi Savall, and her work with Mary Springfels and Chicago's Newberry Consort resulted in ¡Ay amor!, a recording of 17th-century Spanish theatrical songs released by Harmonia Mundi. At present she is readying her performing edition of Celos aun del aire matan (Madrid, 1660) for publication, and writing about the first Hispanic operas, musical eroticism, and the politics of opera production in Madrid, Rome, Naples, and Lima in the late seventeenth century.  Recent seminars have focused on the operas of Alessandro Scarlatti.