Faith-based organisations (FBOs) play a vital role in development across sub-Saharan Africa, particularly where state capacity is limited. However, existing scholarship has paid insufficient attention to how historical institutional trajectories shape the capacities of Christian and Muslim organisations operating within the same context. This article addresses that gap through a comparative qualitative study of faith-based development in Northern Ghana, drawing on semi-structured interviews, focus group discussions, participant observation, and documentary analysis. The findings reveal that differences in organisational effectiveness are rooted more in historical institutional development than in theological distinctions. Christian organisations continue to benefit from long-standing missionary investments in education, healthcare, administration, and international partnerships, while Muslim NGOs have largely emerged through entrepreneurial models characterised by adaptive governance, transnational philanthropy, digital mobilisation, and diaspora engagement. These contrasting trajectories produce unequal capacities in funding, institutional resilience, and programme sustainability, yet also generate complementary strengths in community participation, cultural responsiveness, and religious legitimacy. Beneficiaries value organisations primarily for service quality, accountability, and trust rather than religious identity. By introducing the concept of asymmetrical institutional architecture, the study provides a historically grounded framework that enriches religion-and-development scholarship and advocates collaborative partnerships that recognise institutional inequalities while leveraging the complementary strengths of Christian and Muslim FBOs.