In 1960 he graduated magna cum laude in history from Harvard College and was awarded a Shaw Traveling Fellowship which he used to explore Europe, the Middle East and Afghanistan.
A Guggenheim Fellowship allowed him to write his first book, Loyalty and Leadership in an Early Islamic Society (1980), the manuscript of which gained him tenure.
The MacArthur award allowed him to write his second book, The Mantle of the Prophet (1985), which was a study of contemporary Iran as understood through two millennia of history.
He was elected a member of the American Academy of Arts and Sciences and the Council on Foreign Relations and has served as a series editor for several academic publishers.
Mottahedeh was the author of numerous articles on a wide range of topics from the Abbasid period in the eighth century to Islamic revival movements of the present day.