The active involvement of church leaders in struggles for political power, the engagement of churches in ethnic politics, and the development of local parishes as centers of power during the colonial era set the pattern for church–state relations in postcolonial Rwanda. Many officials in the First Republic, including President Kayibanda, were proteges of the Catholic Church who, while occasionally clashing with church leaders as they sought to assert their political independence, maintained close personal and official ties with the Catholic hierarchy. The military personnel who assumed power in a 1973 coup did not owe the same political debt to the Catholic Church as their civilian predecessors, but appreciating the power of the church, the new president, Juvenal Habyarimana, made clear his own position as a devout Catholic and quickly sought to develop strong ties between his regime and both Catholic and Protestant church leaders. Church leaders, for their part, embraced the new regime and continued to teach obedience to political authorities.

Just as in an earlier generation some missionaries challenged the decision of the Catholic leadership to ally the church with the Tutsi and the royal court, during the Habyarimana regime some segments of the churches objected to the alliance of the churches with an authoritarian state and the integration of churches into structures of power that benefited the rich. During the 1980s, the influence of liberation theologies, church institutional reforms, the expansion and reconceptualization of church-sponsored development activities, and the emergence of new church-related organizations and movements fostered the growth of a democratic sentiment within the churches.