This study examines the Qur’an schools in Malay Peninsula during the British colonial rule. It investigates how these educational institutions were perceived by the colonial rule and analyse the process of their transformation over the decades. It is also crucial to clarify the concept of Qur’an schools within the juncture of overall Islamic education centers operated not only in Malaya but also in the Archipelago, which were functional enough in the dissemination of traditional religious knowledge and values to the new generations. The colonial rule delivered new educational initiatives such as the Malay vernacular schools by implimenting various policies on the basis of a Euro-centric approach in the latter period of colonial rule. The colonial rule integrated Qur’an classes emulating partially the practice of Qur’an schools into newly established Malay vernacular schools in order to attract the interests of the Malay parents in an effort to convince them to send their children to these institutions. Although Malay families got used to these new education initiatives and register their children at these institutions, it is asserted that the secular-based vernacular schools are deemed to have caused degradation in the socio-cultural and religious structure of traditional Malay Muslim societies. In this context, this new education system is a subject matter to be studied and analyzed as a phenonemon of change in social structure. It is also worth observing the reactions of the Malay Muslim communuities during this process towards the new educational establishment. The analytical narratives of this study rely on sources produced during the colonial period and other related sources of contemporary literature.