Many African Independent Churches emerged during the colonial era in central Kenya and western Nigeria. At times they were opposed by government officials and missionaries. Most scholars have limited the field of enquiry to the flash-points of this encounter, thereby emphasizing the relationship at its most severe. This study questions current assumptions about the encounter which have derived from these studies, arguing that both government and missionary officials in Kenya and Nigeria exhibited a broader range of perspectives and responses to African Independent Churches. To characterize them as mainly hostile to African Independent Churches is inaccurate. This study also explores the various encounters between African Independent Churches and African politicians, clergymen, and local citizens. While some scholars have discussed the positive role of Africans in encouraging the growth of independent Christianity, this study will discuss the history in greater depth and complexity. The investigation will show the importance of understanding the encounter on both a local and national level, and the relationships between the two. It is taken for granted that European officials had authority over African leaders, but in regard to this topic many Africans possessed a largely unrecognized ability to influence and shape European perceptions of new religious movements. Finally, this thesis will discuss how African Independent Churches sometimes provoked negative responses from others through confrontational missionary methods, caustic rhetoric, intimidation and even violence. These three themes resurface throughout the history of the encounter and illustrate how current assumptions can be reinterpreted. This thesis suggests the necessity of expanding the primary scholarly focuses, as well as altering the language and basic assumptions of the previous histories of the encounter.