Joan Afferica's research fields include elite formation in 17th- and 18th-century Russia, politics of Soviet historiography, and Russian and Soviet imperial history. Her work on the formation of the Hermitage Collection of Russian Books and Manuscripts was published in the Soviet Union and Germany.

She presented 11 lectures (1995–97) in the winter lecture series on Russian history and culture inaugurated at the Armory Palace in the Moscow Kremlin following the collapse of the Soviet Union. These led to the introduction for Smith students to an interterm course on Russian history and culture conducted on-site in the palaces, churches and museums of the Kremlin.

Afferica has introduced the West to the work of the exiled Soviet artist E. P. Rozengolts, with two exhibitions at The National Museum of Women in the Arts (1999) and The New York Studio School of Drawing, Painting and Sculpture (2001). Her translation of a book of reproductions of the Rozengolts works recently appeared in Moscow. She is completing a translation and commentary of S. M. Solovev’s history of the uprising of Bogdan Khmelnitsky (1648–57).