The debate on integration of shade trees on farmers’ fields is lately becoming more pronounced due to the increasing land fragmentation, particularly in the highlands where the number of trees on farm is reducing drastically. In these farmlands, the choice of shade trees is the result of complex farmers’ analyses and valuation of tradeoffs among the increasing productivity, socioeconomic and environmental benefits. However, little is known about what coffee farmers specifically base their decisions on to select and grow shade trees in their fields. This study therefore identified the key reasons behind farmers’ choices of use of shade trees in coffee fields on Mount Elgon, Eastern Uganda using the Unified Theory of Use and Acceptance of the Technology framework. A cross-sectional study was conducted with 120 respondents and complimented with focus group discussions. A Structural Equation Modelling technique was conducted to examine the usage of shade trees. Results show facilitating conditions also known as institutional factors were significant in explaining the choices of farmers to use shade trees, with the effect stronger on soils of low fertility. Effort expectancy and social influence only marginally influenced use. The model explains 69% of the variance in choice to use shade trees in coffee agroforestry systems. Mediation by soil fertility, gender and experience explain 23%, 16%, and 4%; respectively. Effort expectancy and the existence of adequate facilitating conditions increased females’ choices to use shade trees. This study underscores the consideration for location specific technology facilitating conditions, social influence and ease of use, for long standing technologies, by farming support institutions, decision-makers and development partners in designing and disseminating sustainable agricultural management strategies for implementation in coffee-based agroforestry systems.