Even before Azazeel won the International Prize for Arabic fiction (or "Arabic Booker") in 2009, copies of the novel were piled high at Cairo's pavement booksellers. Its unusual setting in early Christian, pre-Islamic Egypt fuelled interest, along with its teasing literary frame, whereby an archaeologist in late 20th-century Syria uncovers 30 confessional scrolls penned by an Egyptian monk some 1,500 years before. But curiosity was soon piqued by controversy, as the Coptic church voiced outrage at the portrayal of St Cyril of Alexandria as a rabble-rousing fanatic.

The novel follows the picaresque passage through faith, doubt, temptation and torment of Hypa, monk, physician and  risibly, to many he meets  poet from southern Egypt. His pilgrim's progress entails whisperings from the devil, and erotic interludes with the widow Octavia, Alexandrian servant of a Sicilian silk merchant, and Martha, a singer. He composes hymns and sleeps seated, in his monastic cell ("There are Egyptian tombs that are larger"). A reluctant witness to the age's terrors, Hypa writes his memoirs in a monastery near Aleppo, at the inner prompting of the accursed Azazeel, otherwise known as Satan or Beelzebub. Though Hypa's mother-tongue is Coptic, he knows Greek and Hebrew, and writes in Aramaic  or Syriac, as the language of Christ becomes known. His humble good nature and bewildered horror are at times reminiscent of Robert Graves's Claudius.

Born in AD391, when Christianity was imposed as Roman Egypt's official religion, the young Hypa travels north to Alexandria, city of "whores and gold", "salt and cruelty", where Christians are no longer a persecuted minority. Pope Cyril sermonises from a gilt pulpit, his gold robes contrasting with the rags of the Christ statue behind him. Cyril sees himself amid sedition, in a holy war against Jews (whom he casts out of the city), heretics, pagans and idolaters. He is also set against science, abhoring "astronomy, mathematics and magic". Its symbol is Hypatia, the historical figure with whom Hypa is briefly infatuated. A neo-Platonist philosopher and mathematician, and a charismatic teacher, she was lynched by a Christian mob in AD415  savagery that Hypa witnesses. In fleeing the city  along with many scholars of the time  he baptises himself Hypa in honour of her.

Hypa is aghast at the violence sweeping the "land of God ... in the name of Christ". Yet as his fatherly mentor in Jerusalem, Bishop Nestorius, points out: "Killing people in the name of religion does not make it religious ... those are people of power not faith." As bishops in the imperial centres of Rome, Alexandria and Constantinople vie for power, and church jostles with state, Hypa plays a humble role as translator in doctrinal rifts and schisms. The nub is whether the Virgin Mary is the mother of God: "Do you believe that Jesus is God, or is He the messenger of God?" Or, as a feverish Hypa imagines Azazeel asking mischievously: "Did God create man, or was it the other way round?" The Syrian-born Nestorius is adamant that "humans do not give birth to gods"  a belief that eventually sees him deposed for heresy. The novel hints that this doctrinal split stems from cultural differences between Greco-Egyptian and desert Arab views of divinity, rather as Hypa still alludes to the ancient god Khnum, who fashioned humans from clay.

The theological wrangling also reflects earthly ambition. Hypa is troubled by his mentor Nestorius's unholy pact with the Emperor Constantine: "Help me in my war on unbelievers and I will help you in your war with Persia. Give me an Earth free of heresy and I will give you the keys to Heaven." Equally troubling is another dogma he finds in a Yemeni monk, who sees femininity and women as the "cause of every misfortune", and abhors singing  especially by girls.

In Jonathan Wright's supple translation there are memorable passages, from a monkey shaking dry dates from a palm, to the perilous pleasure of swimming in the buoyant sea rather than the crocodile-infested Nile. Yet, if the novel often lacks descriptive richness, its strength lies in its ingenuous narrator and the resonant play of ideas. Youssef Ziedan, a scholar who founded the manuscript centre and museum at the New Library of Alexandria, knows his sources. Through late antiquity, he explores humane views of sexual passion and women's learning, and exposes violence perpetrated in the name of the sacred. As for dogma, the novel suggests how seemingly immutable doctrines are shaped by the beliefs they purport to leave behind.

Literary awards thrive on controversy, and in 2009 the Egyptian writer Youssef Ziedan caused plenty in his homeland when Azazeel won the International Prize for Arabic Fiction. Ostensibly the memoirs of a fifth-century doctor-monk named Hypa, whose scrolls bearing witness to a period of Christian turmoil are uncovered in 1994, its depictions of an aggressive, pagan-purging Bishop Cyril offended some members of the Coptic Church so gravely that they filed lawsuits.

Distance and secularity suggest most English-speaking readers are likely to approach the novel (superbly translated by Jonathan Wright) with slightly less baggage. And, in fact, for all the trouble caused by his expertly researched nods to the internecine struggles within the nascent church, Ziedan seems to be calling for harmony and understanding in religious thought. He merely underlines how ridiculous  and yet dangerous  squabbles between religious sects can be.

All of which makes it easy to forget that Azazeel is actually a novel. Happily, it's underpinned by a believably human and universal tale of a man, racked with doubt and temptation, on a journey to find himself. Still, Hypa's story starts painfully slowly  it's not until the monk sails up the Nile to Alexandria that it gains any forward momentum. There, he meets Octavia and succumbs to "forbidden pleasures"  embarrassingly florid ones, if truth be told  before witnessing the murder by Cyril's followers of the real-life "pagan" mathematician Hypatia.

Hypa leaves Alexandria, heartbroken, and spends the rest of the novel scratching around the Holy Land, perplexed by life, religion, medicine, the devil Azazeel, and women. Sometimes this sense of drift and uncertainty is mirrored in the storytelling  we're told on more than one occasion that "days and months passed tediously". Such is the life of a monk, perhaps.

Yet in the end, Hypa's naivety is a strength: he's a strange, unnerving yet compelling hero-narrator, a blank canvas through which Ziedan vividly explores the time. The writing, too, is unflashy and sincere, neatly matching the monasticism at the book's heart. The prize, or the controversy that followed, might explain why it's sold more than a million copies in Egypt. But it's the lasting image of Hypa, a man continually questioning the meaning of life, that really strikes home.