Allegro started to train for the Methodist ministry but transferred to graduate with a first class degree in Semitic Studies from the University of Manchester. He obtained an M.A. for a study into the Balaam Oracles and later pursued further research, studying the various dialects of Biblical Hebrew at Oxford. In 1953 he was invited to become the first British representative on the international team working on the recently discovered Dead Sea Scrolls from cave 4 in Jordan. The following year he was appointed assistant lecturer in Comparative Semitic Philology at Manchester, and held a succession of lectureships there until he resigned in 1970 to become a full-time writer. In 1961 he was made Honorary Adviser on the Dead Sea Scrolls to the Jordanian government.