Evaluation of agricultural Research, Development, Extension and Management requires knowledge of farming systems economics and risk as well as broader adoption drivers. However, these factors are not often effectively combined when determining the success of agricultural research projects. To fill this gap, we developed Value-Ag, an integrated modelling framework that combines bioeconomic simulation, risk analysis, adoption theory, and impact assessment to inform smallholder transition to sustainable farming in the context of production risk and household dynamics. We use a case study of sustainable intensification in the salt-affected coastal zones of Bangladesh and West Bengal, India to illustrate Value-Ag’s potential to evaluate agricultural innovations in a rigorous, systematic, and participatory manner across a range of agroecological and socioeconomic contexts. The process aims to stimulate thinking and learning opportunities with the relevant stakeholders and increase the scrutiny of projects so that they deliver greater value for money while fostering a more results-focused culture.