This chapter explores the complex encounter between the missionaries of the Basel German Missionary Society (BM) and local children raised in their boarding schools/orphanages based at various parts of British-ruled Malabar in present-day south India. The BM played an instrumental role in establishing the earliest residential institutions for the children of the labouring poor in the Malayalam speaking region where they sought to also forge ‘model’ Christian communities. Poor, colonized children belonging to lower caste communities were targeted for conversion, which resulted in varying contestations about childhood. In their attempt to erase previous caste-inscribed markers, the missionaries negotiated with local power dynamics and sites of authority, and the children themselves. Often, ‘orphans’ were not always without parents, and the BM employed coercive measures to admit poor children into their orphanages, by arguing against the so-called ‘barbarity’ of Indian parenting, and reorienting norms of childhood. They were not entirely successful as children also influenced decision-making processes and resisted the rigorous disciplinary order and labour regime inflicted on them. This chapter attempts to trace the politics of these boarding institutions and demonstrates ambiguity and racial tension marking the missionary project of schooling poor children in colonial south India even as Christianity brought new ideas of morality and self. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.