Allen has written several books. He is the author of two biographies of Pope Benedict XVI. The first was written before then-Cardinal Joseph Ratzinger became pope, the other after his election to the papacy. In 2000, Allen published "Cardinal Ratzinger: The Vatican's Enforcer of the Faith", the first biography of Ratzinger in English. Several reviewers criticized it as being biased against Ratzinger. Joseph Komonchak called it "Manichaean journalism." After some examination, Allen concluded that this criticism was valid. In his next biography of Ratzinger, "The Rise of Benedict XVI: The Inside Story of How the Pope Was Elected and Where He Will Take the Catholic Church" (2005), Allen tried to be fair to all sides and viewpoints. Allen acknowledged that his first book was "unbalanced" because it was his first book and was written, he wrote, "before I arrived in Rome and before I really knew a lot about the universal church." In that acknowledgement he said the first biography "gives prominent voice to criticisms of Ratzinger; it does not give equally prominent voice to how he himself would see some of these issues."