Efforts of national governments and international agencies aimed at alleviating hunger and poverty are often undermined by lack of long-term adoption of agricultural innovations. Studies commonly explain farmers’ adoption decisions using household general determinants, yet decision-making, particularly for under-resourced smallholder farmers in sub-Saharan Africa, is a complex process. Using the case of conservation agriculture [CA], this article analyses dis-adoption of agricultural technologies by examining multiple domains of Malawi’s CA innovation system and how these influence farmer decision-making. It analyses institutional arrangements of CA promoters, national policies and farmers’ experiences. From this, we empirically derive a multifaceted dis-adoption drivers’ framework to explain CA dis-adoption in smallholder farming systems. Our findings reveal that adverse features in national policies, institutional arrangements, technological attributes and social cultural dimensions all lead to unfavourable experiences of CA for smallholder farmers, which can culminate in dis-adoption. The CA dis-adoption drivers’ framework we develop in this study provides a useful troubleshooting tool. It can be used to guide improvements in the design and implementation of project-based interventions seeking long-term adoption of agricultural innovations across sub-Saharan Africa.