Through the use of cost–consequence analysis (CCA), a recent evaluation of a Millennium Villages Project (MVP) in Ghana revealed it to have represented poor value for money (VFM), with comparator projects elsewhere seeming to deliver similar results at less than half the cost. However, complex integrated development programmes (IDPs) such as the MVP pose serious challenges for VFM assessments. IDPs target system-wide changes in resource-scarce contexts, making expensive foundational investments in infrastructure and other systems. The unit costs of benefits will tend to be high in the short or medium term. In contrast, many standalone projects, showing greater efficiency, may target similar outcomes, but do so by building upon existing prior investments. In this article, comparing three VFM approaches, we argue that CCA is the most appropriate for IDPs. However, its applications must be mindful of the contextual differences in which the comparator standalone projects and the IDP were implemented.