Beinin's research and writing focuses on workers, peasants, and minorities in the modern Middle East. Though initially interested in the rise of an Arab Working class in Mandatory Palestine, under his thesis supervisor's advice, he changed the topic of his doctoral thesis to a history of the Egyptian labor movement since 1936. That Ph.D. thesis was combined with one covering an earlier period of Egyptian labor history by his friend and colleague Zachary Lockman and resulted in the publication of "Workers on the Nile: Nationalism, Communism, Islam and the Egyptian Working Class, 1882–1954" (1989). Among his later work is a study of the Jewish communities of modern Egypt which led to his major historical study, "The Dispersion Of Egyptian Jewry: Culture, Politics, And The Formation Of A Modern Diaspora" (1998), which examines the diversity of Egyptian Jewish identities in Egypt and in the diaspora. He has engaged in fieldwork to collect oral reports among many Egyptian Jewish communities dispersed throughout the world after the Suez War of 1956, among them the Karaites of San Francisco.