The uptake of innovative technologies and practices in agriculture aimed at the valorisation of natural resources can be scant in Low and Middle Income Countries (LMICs). Integration of financial viability assessments with farmers and environmental evaluations can help to understand some aspects of the low uptakes of innovations. Using the case study of Cocoa Pod Husk (CPH) valorisation in Indonesia, we provide insights into (i) a choice modelling method to assess the economic viability of CPH valorisation and (ii) an agronomic trial assessing the consequences on soil quality of diverting CPH from its role as a natural fertilizer. The economic viability assessment suggested that farmers require higher levels of compensation than might be expected to collect or process CPH (a small proportion of farmers would undertake all processing activities for 117 GBP/t CPH). The agronomic trial concluded that CPH plays only a minor role in the maintenance of soil phosphorus, calcium and magnesium, but it plays an important role for crop potassium. CPH removal would reduce the partial balances for carbon and nitrogen by 15.6% and 19.6%, respectively. Diversion of CPH from current practices should consider the long-term effects on soil quality, especially because it might create increased reliance on mineral fertilizers.