Improving the livelihoods of communities living in fragile ecosystems, such as tropical forests, is among the main strategies to promote their conservation and preserve wildlife. In the Ecuadorian Amazon, farmers’ cooperatives are recognized as an important mechanism to improve the socioeconomic conditions of local communities. This study analyzes the integration of pyrolysis processes to convert agricultural waste into biochar as a way to implement the bioeconomy in these organizations. We found that post-harvesting processes in the studied farmers’ cooperatives are similar, and coffee husks are a potential feedstock to produce biochar. Although the environmental policies in Ecuador consider the valorization of agricultural waste, we did not find any specific standard to regulate the operation of pyrolysis facilities. Nonetheless, conversion of agricultural waste into biochar can contribute to (i) replacement of subsidized fossil fuels used in drying processes, (ii) prevention of environmental pollution caused by accumulation of waste, (iii) emergence of new income sources linked with the provision of carbon sequestration services, and (iv) the long-term maintenance of soil fertility. Currently, demonstration projects are needed to stimulate collaboration among farmers’ cooperatives, academia, the government, international cooperation agencies, and existing forest conservation initiatives.