The coexistence of the need to improve economic conditions and the conscious use of environmental resources plays a central role in today’s sustainable development challenge. In this study, a novel integrated framework to evaluate the impact of new technological interventions is presented and an application to smallholder coffee farms and their supply chains in Kenya is proposed. This methodology is able to combine multiple information through the joint use of three approaches: supply chain analysis, input-output analysis, and energy system modeling. Application to the context of the Kenyan coffee sector enables framework validation: shading management measures, the introduction of eco-pulpers, and the exploitation of coffee waste biomass for power generation were compared within a holistic high-level perspective. The implementation of shading practices, carried out with fruit trees, shows the most relevant effects from the economic point of view, providing farmers with an additional source of income and generating $903 of work for every million of local currency (about $9k) invested in this solution. The same investment would save up to 1.46 M m³ of water per year with the eco-pulpers technology. Investing the same amount in coffee-biomass power plants would displace a small portion of production from heavy-duty oil and avoid importing a portion of fertilizer, saving up to 11 tons of CO₂ and around $4k per year. The results suggest the optimal allocation of a $100m budget, which can be affected by adding additional constraints on minimum environmental or social targets in line with sustainable development goals.