The extreme popularity of FitzGerald's work led to a prolonged debate on the correct interpretation of the philosophy behind the poems. FitzGerald emphasized the religious skepticism he found in Omar Khayyam. In his preface to the Rubáiyát, he describes Omar's philosophy as Epicurean and claims that Omar was "hated and dreaded by the Sufis, whose practice he ridiculed and whose faith amounts to little more than his own, when stripped of the Mysticism and formal recognition of Islamism under which Omar would not hide". Richard Nelson Frye also emphasizes that Khayyam was despised by a number of prominent contemporary Sufis. These include figures such as Shams Tabrizi, Najm al-Din Daya, Al-Ghazali, and Attar, who "viewed Khayyam not as a fellow-mystic, but a free-thinking scientist".:663–664 The skeptic interpretation is supported by the medieval historian Al-Qifti (ca. 1172–1248), who in his The History of Learned Men reports that Omar's poems were only outwardly in the Sufi style, but were written with an anti-religious agenda. He also mentions that Khayyam was indicted for impiety and went on a pilgrimage to avoid punishment. Critics of FitzGerald, on the other hand, have accused the translator of misrepresenting the mysticism of Sufi poetry by an overly literal interpretation. Thus, the view of Omar Khayyam as a Sufi was defended by Bjerregaard (1915).Dougan (1991) likewise says that attributing hedonism to Omar is due to the failings of FitzGerald's translation, arguing that the poetry is to be understood as "deeply esoteric".
Idries Shah (1999) similarly says that FitzGerald misunderstood Omar's poetry.
The Sufi interpretation is the view of a minority of scholars. Henry Beveridge states that "the Sufis have unaccountably pressed this writer [Khayyam] into their service; they explain away some of his blasphemies by forced interpretations, and others they represent as innocent freedoms and reproaches". Aminrazavi (2007) states that "Sufi interpretation of Khayyam is possible only by reading into his Rubaiyat extensively and by stretching the content to fit the classical Sufi doctrine".:128
FitzGerald's "skepticist" reading of the poetry is still defended by modern scholars. Sadegh Hedayat (The Blind Owl 1936) was the most notable modern proponent of Khayyam's philosophy as agnostic skepticism. In his introductory essay to his second edition of the Quatrains of the Philosopher Omar Khayyam (1922), Hedayat states that "while Khayyam believes in the transmutation and transformation of the human body, he does not believe in a separate soul; if we are lucky, our bodily particles would be used in the making of a jug of wine". He concludes that "religion has proved incapable of surmounting his inherent fears; thus Khayyam finds himself alone and insecure in a universe about which his knowledge is nil". In his later work (Khayyam's Quatrains, 1935), Hedayat further maintains that Khayyam's usage of Sufic terminology such as "wine" is literal, and that "Khayyam took refuge in wine to ward off bitterness and to blunt the cutting edge of his thoughts."