This article argues that the emerging Cognitive Science of Religion (CSR) provides a valuable new perspective on colonialism. CSR argues that humans are innately inclined towards certain types of religious belief (e.g., belief in spirit beings, belief in immortal souls) and certain types of non-utilitarian morality (e.g., belief in an obligation to care for kin, belief in an obligation to avoid ‘disgusting’ substances or behaviours). These innate inclinations underlie many religious and cultural traditions transformed by colonialism, including Islam. The article suggests that colonial power operates not only by suppressing traditional non-Western institutions but also by suppressing the natural inclinations underlying non-Western traditions. This claim is developed through a study of colonial efforts to transform Egypt’s al-Azhar, the world’s most influential institution of Islamic learning and scholarship. These efforts made al-Azhar into the centre of a global Islamic reform movement, which sought to integrate Islam with a colonial scientific-utilitarian worldview.