Bioenergy recovery from biomass by-products is a promising approach for the circular bioeconomy transition. However, the management of agri-food by-products in stand-alone treatment facilities is a challenge for the low-capacity food processing industry. In this study, the techno-economic assessment of a small-scale anaerobic digestion process was evaluated for the management of jabuticaba by-product and the production of biomethane, electricity, heat, and fertilizer. The process was simulated for a treatment capacity of 782.2 m3 y−1 jabuticaba peel, considering the experimental methane production of 42.31 L CH4 kg−1 TVS. The results of the scaled-up simulated process demonstrated the production of biomethane (13,960.17 m3 y−1), electricity (61.76 MWh y−1), heat (197.62 GJ y−1), and fertilizer (211.47 t y−1). Economic analysis revealed that the process for biomethane recovery from biogas is not profitable, with a net margin of −19.58% and an internal rate of return of −1.77%. However, biogas application in a heat and power unit can improve project feasibility, with a net margin of 33.03%, an internal rate of return of 13.14%, and a payback of 5.03 years. In conclusion, the application of small-scale anaerobic digestion can prevent the wrongful open-air disposal of jabuticaba by-products, with the generation of renewable energy and biofertilizer supporting the green economy toward the transition to a circular economy.