Muslim and Christian faith-based organisations (FBOs) have become influential partners in advancing education, healthcare, poverty reduction, humanitarian assistance, and community development across sub-Saharan Africa. Despite their growing significance, limited comparative research has examined how these organisations negotiate religious diversity while implementing development programmes in pluralistic societies. This article investigates the experiences of Muslim and Christian non-governmental organisations (NGOs) in Northern Ghana. Employing a qualitative comparative design, the data were generated through semi-structured interviews, focus group discussions, participant observation, and documentary analysis. The findings reveal that although Muslim and Christian NGOs are guided by distinct theological traditions and historical trajectories, both increasingly adopt inclusive development approaches centred on human dignity, social justice, community participation, and sustainable livelihoods. Organisational legitimacy depends more on transparency, accountability, cultural sensitivity, and community trust than on religious affiliation. Nevertheless, donor disparities, historical mistrust, and perceptions of proselytisation continue to shape inter-organisational relations. The article concludes that effective interfaith engagement enables Muslim and Christian NGOs to transform religious diversity into a resource for collaboration, social cohesion, and sustainable development in religiously plural societies.