The mission experienced growing tensions between African agents and European missionaries, driven by issues of discipline and clashes in cultural attitudes. Some European missionaries viewed themselves as superior, which led to friction with African leaders who sought dignity and recognition. These tensions came to a head during a review of mission discipline, resulting in disagreements that left both sides dissatisfied.
As a consequence, a split emerged within the mission. Leadership in Onitsha became primarily European, while African leadership was established in the Delta, beginning with Dandeson Crowther, the son of Bishop Crowther.
European missions operated within hierarchical structures and were centrally controlled by home boards. Although some Africans were initially promoted to leadership positions—most notably Bishop Samuel Ajayi Crowther in Nigeria—they were often later sidelined or undermined by white missionaries who believed Africans were not yet ready for full autonomy. This lack of recognition of African leadership capacity became a major point of contention.
The broader colonial context further shaped these dynamics. European missionaries were closely associated with colonial powers, creating complex relationships. While some missionaries genuinely sought to spread their faith, their presence was frequently intertwined with colonial agendas, contributing to perceptions of Christianity as an instrument of foreign influence.