In recent years, there has been a renewed interest in the politics of religious freedom in non-Western societies, particularly in Muslim-majority countries. Many of these countries such as Indonesia and Egypt have established religious freedom clauses in their constitutions that protects the rights of religious minorities to establish places of worship and practice their religion without any interference from both the state and from other religious groups. However, despite these constitutional guarantees, there has been a rise of incidents of inter-religious conflicts in the two countries within the past decade, affecting Christians and members of the Ahmadiyah minority sects in Indonesia and the Coptic Christian community in Egypt. These incidents have often been attributed to the rise of Islamic fundamentalism and revivalist Islamic social movements in the political realm of these countries. This paper argues that Islamic fundamentalism is not sufficient in explaining the rise of inter-religious conflict in Indonesia and Egypt. Instead, they occurred due to the coalitional pacts and alliances between Christian minorities to support authoritarian rulers (Indonesia’s Suharto and Egypt’s Hosni Mubarak) that suppressed Muslim political activists in both countries. The tacit supports of Christian political and economic elites in both societies, whom backed the oppressive ruling regimes in their respective societies, along with the lack of support they have given to Islamic pro-democracy activists, have caused alienation between Muslims and Christians in both societies. These helped to fuel the call from revivalist Muslims to curb the religious privileges of Christians in both Indonesia and Egypt, and in-turn increased the incidents of conflicts and violence between the two religious groups. This study uses comparative historical methodology to find the empirical data to support its theoretical arguments. First, it outlines the history of the establishments of Indonesian and Egypt constitutions and how both Muslims and Christians agreed to the religious freedom clauses in the constitutions of these societies. Second, it explores why Christians decided to form an alliance with the authoritarian regimes in both societies in order to retain their political and economic privileges, while alienating the Muslim-majority groups in the process. Third, it shows how these alliances helped to contribute to the inter-religious conflicts between the two religious groups that increased during the transition process that ended the Suharto and Mubarak regimes and continued to worsen afterwards.