The paper examines the transformation of Islamic identity of Muslim students in southwest Nigeria from the late colonial period up to the 2000s. In 1954, Muslim students attending schools run by Christians in Lagos established the Muslim Students’ Society (MSS) as an associational group which encouraged the development of Islamic identity among them. Their objective was to preserve their religious identity through a range of social, educational and religious activities in the schools. This reflected their understanding of Islam based on every day Muslim practices especially on prayers, Qur’an memorisation, rules of fasting and festivals. However, this has changed since the 1980s as Islam began to be understood as a comprehensive way of life. The transformation which was part of the reform movement in the global Muslim community led to the emergence of diverse and often conflicting practices in MSS and students who are more conscious about piety and less tolerant of non-Muslims. MSS contested other Muslim practices, traditional beliefs and became more engaged in knowledge production in this period. The change is obvious among female students who abandoned the local Muslim women dressing for ijab (headscarf) and niqob (veil). Using historical and ethnographic data, this paper will thus consider the change in the understanding of Islam in MSS and its impact on new expression of orthodox Islamic identity among Muslim students. How this change affected socio-religious encounters in southwest Nigeria will also be discussed.