Abstract Background Understanding the cost-effectiveness and affordability of interventions to reduce maternal and newborn deaths is critical to persuading policymakers and donors to implement at scale. The effectiveness of community mobilisation through women’s groups and health facility quality improvement, both aiming to reduce maternal and neonatal mortality, was assessed by a cluster randomised controlled trial conducted in rural Malawi in 2008–2010. In this paper, we calculate intervention cost-effectiveness and model the affordability of the interventions at scale. Methods Bayesian methods are used to estimate the incremental cost-effectiveness of the community and facility interventions on their own (CI, FI), and together (FICI), compared to current practice in rural Malawi. Effects are estimated with Monte Carlo simulation using the combined full probability distributions of intervention effects on stillbirths, neonatal deaths and maternal deaths. Cost data was collected prospectively from a provider perspective using an ingredients approach and disaggregated at the intervention (not cluster or individual) level. Expected Incremental Benefit, Cost-effectiveness Acceptability Curves and Expected Value of Information (EVI) were calculated using a threshold of $780 per disability-adjusted life-year (DALY) averted, the per capita gross domestic product of Malawi in 2013 international $. Results The incremental cost-effectiveness of CI, FI, and combined FICI was $79, $281, and $146 per DALY averted respectively, compared to current practice. FI is dominated by CI and FICI. Taking into account uncertainty, both CI and combined FICI are highly likely to be cost effective (probability 98% and 93%, EVI $210,423 and $598,177 respectively). Combined FICI is incrementally cost effective compared to either intervention individually (probability 60%, ICER $292, EIB $9,334,580 compared to CI). Future scenarios also found FICI to be the optimal decision. Scaling-up to the whole of Malawi, CI is of greatest value for money, potentially averting 13.0% of remaining annual DALYs from stillbirths, neonatal and maternal deaths for the equivalent of 6.8% of current .