Following the events of 9/11, many misconceptions entered the policy-making platform with regard to the need for education reforms in the Muslim world. Based upon Western cultural and societal norms and increased scepticism of the role of religion in violence, these assumptions have triggered a strong wave of calls for a top-down approach to reform formal state schools in predominantly Muslim countries, These calls often meet with resistance at national and community levels. This article seeks to examine these misconceptions and investigate why educational reform efforts through top-down frameworks which are especially motivated by countering violent extremism or terrorism have had only limited success. Many major international intergovernmental organisations, non-governmental organisations and governments have invested time and effort into education measures aiming to build peace and coexistence in Muslim countries, but they have been unable to build a relationship of trust with community leaders and school authorities. The authors argue that the main reason for defiance is reformers' failure to closely examine the cultural context of their chosen setting and work with existing tools and local institutions. Illustrating their point with a case study of an intervention carried out in informal Qur'anic schools in Niger, West Africa, the authors offer an alternative method which fosters changes from within. They argue that this model has a better chance of sustainability and could thus be used as the basis for future interventions.