Coconut (Cocos nucifera) is one of the most economically significant tropical crops in coastal regions of the Global South, including Colombia, where it is primarily cultivated by small-scale producers. However, its processing generates large amounts of lignocellulosic residues, particularly coconut shells, which are often underutilized despite their high potential as a renewable energy source. In this context, the development of sustainable and decentralized thermal energy systems is essential to enhance the competitiveness of rural agroindustries. This study presents the design and experimental evaluation of a biomass-based boiler using coconut shell as fuel, within the framework of the Biopalmas program in Colombia. A systematic design methodology was implemented considering the thermal energy requirements of agroindustrial processes such as vacuum frying and tangential microfiltration, while promoting circular economy principles through waste valorization. Experimental tests were conducted to evaluate combustion performance, energy efficiency, and emissions. The system achieved an average combustion efficiency of 87.2%, indicating effective fuel oxidation, although the presence of CO and CH₄ in flue gases revealed partial combustion limitations associated with air–fuel mixing and residence time. The boiler delivered an average thermal power of 452.9 kW, with 305.7 kW effectively transferred to the working fluid, resulting in a global thermal efficiency of 67.5%. Energy losses were mainly associated with incomplete combustion (≈57.6 kW) and sensible heat in flue gases (≈89.7 kW), highlighting opportunities for improvement through air supply optimization and heat recovery strategies. Emission analysis showed low NOx levels, while CO emissions indicated the need for improved combustion control. The results demonstrate the technical feasibility and operational stability of coconut-shell-based systems as a scalable solution for sustainable thermal energy supply in rural agroindustrial applications.