Maternal and neonatal mortality are unacceptably high in developing countries. Essential nutrition interventions contribute to reducing this mortality burden, although nutrition is poorly integrated into health systems. Universal health coverage is an essential prerequisite to decreasing mortality indices. However, provision and utilization of nutrition and health services for pregnant women and their newborns are poor and the potential for improvement is limited where health systems are weak. The Community-Based Maternal and Neonatal Health and Nutrition project was established as a set of demonstration projects in 4 countries in Africa with varied health system contexts where there were barriers to safe maternal health care at individual, community and facility levels. We selected project designs based on the need, context, and policies under consideration. A theory driven approach to programme implementation and evaluation was used involving developing of contextual project logic models that linked inputs to address gaps in quality and uptake of antenatal care; essential nutrition actions in antenatal care, delivery, and postnatal care; delivery with skilled and trained birth attendant; and postnatal care to outcomes related to improvements in maternal health service utilization and reduction in maternal and neonatal morbidity and mortality. Routine monitoring and impact evaluations were included in the design. The objective of this paper is to describe the rationale and methods used in setting up a multi-country study that aimed at designing the key maternal and neonatal health interventions and identifying indicators related to inputs, outcomes, and impact that were measured to track change associated with our interventions.