Many early Muslim narratives about prophets and their disciples can be relegated to the realm of hagiography rather than history. The edifying and polemical purposes for which these texts were written complicate and sometimes obstruct any attempt to yield historical facts from such texts. This is most apparent in narratives about supernatural miracles ordinarily considered physically impossible by readers. Faithful Muslims generally assumed such miracles to be exceptions to a natural order of the world. However, a small number of Muslim thinkers, both medieval and modern, have denied the historicity of such miracles. The following study examines the work of exegetes of the Quran who viewed themselves as philosophers and modernists to document their attempts to explain miracles attributed to Israelite prophets mentioned in the Quran. Their alternative interpretations broke with medieval and Sunni orthodox views on the subject by interpreting miracles so they did not contradict accepted views of the natural, physical world. Twentieth-century naturalist interpretations of miracles in the Quran seems to have followed identical attempts among nineteenth-century Christians to reinterpret the miracles of Christ as empirically plausible events. What parallels exist between exegetes of Christian and Muslim scripture who opted to interpret miracles with naturalist and allegorical interpretations? When these authors interpreted miracle narratives of the Quran as allegories, how did this affect their understanding of miracles that appear in other genre like hadith and military history (maghazi)? To answer these questions, I examine the work of two Ismailis, al-Qadi al-Nu‘man (d. 974) and Ja‘far b. Mansur al-Yaman (d. 990) and compare their views to those of modernist exegetes writing in the twentieth century. Such a study illuminates the intellectual history of minorities in the Islamic tradition who appear to share some of the same assumptions and sensibilities of contemporary historians about the world around them.