Contemporary ecology and agronomy point to the many benefits of agroforestry crop systems for the provision of ecosystem services by regenerating native ecologies, and in many contexts, socio-economic benefits for coffee farmers, especially the contribution of nitrogen-fixing trees’ litter to soil nutrition and water retention. However, the implementation of agroforestry in coffee cultivation is thus far incomplete and uptake has been uneven. In this paper, we examine the adoption and non-adoption of agroforestry coffee growing techniques as a reflection of the historical, social and cultural embeddedness of smallholder coffee cultivation. It is structured as a narrative literature review contextualized with the results of surveys of smallholder coffee farmers in Colombia, Malawi and Uganda regarding their perceptions of agroforestry coffee in their respective contexts. Findings suggest that coffee farmers’ perceptions of agroforestry and the decision to implement or remove it are influenced by factors included in the notion of embeddedness, involving social relations, historical memory and formal and informal institutions, as well as practical capabilities. Intention and action are sometimes discordant due to the complex interactions of these institutional factors, and they often conflict with outside interveners’ expectations based on epistemological differences. The study illuminates some of the main sources, manifestations and dimensions of the social embeddedness of agricultural practices which mediate the perception of current practices, the sacrifice implied by potential changes, the credibility of theories linking action with outcome and the desirability of expected outcomes.