His research interests include social history of the early modern and modern Middle East, the Ottoman Empire, non-Muslims under Islamic rule, Sephardi Jewry, and natural disasters. He is currently writing a book about natural disasters in the Middle East, and serves as the editor for the Ottoman Empire and Modern Turkey section of the Encyclopedia of Jews in the Islamic World. Ayalon has also taught Middle East and Jewish history at the University of Oklahoma. He earned a BA in education and Middle East history from Tel Aviv University in 2002, and a PhD in Near Eastern Studies from Princeton University in 2009.