Missionaries were major providers of education to Indigenous peoples in the colonial world. They hoped both to convert their pupils to Christianity as well as to ensure that their converts had a Christian environment in which aspects of Western education were taught within the class room. The relationship between missionaries, Governments and Indigenous peoples was, however, often strained as has been demonstrated in Part I of this two‐part article, which examined various responses in different geopolitical and social settings to missionary education. Part II examines some of the scholarly debates and research directions surrounding how missionaries, as some of the first as well as the longest serving providers of education to Indigenous peoples, transmitted and instilled Western notions of race, class and gender to those peoples amongst whom they worked. Although the study of missions has received increased attention in the last few decades within areas such as anthropology, gender studies, post‐colonial studies and area studies, there are still many aspects of missionary schooling that remain understudied. This research overview therefore also provides some future directions for the study of missionaries and their education of Indigenous and non‐European peoples in the long 19th century.