Thermal co-processing of lignocellulosic and aquatic biomass, such as algae and shellfish waste, has shown synergistic effects in producing value-added energy products with higher process efficiency than the traditional method, highlighting the importance of scaling up to pilot-scale operations. This article discusses the design and operation of pilot-scale reactors for torrefaction, pyrolysis, and gasification, as well as the key parameters of co-processing biomass into targeted and improved quality products for use as fuel, agricultural application, and environmental remediation. Techno-economic analysis reveals that end product selling price, market dynamics, government policies, and biomass cost are crucial factors influencing the sustainability of thermal co-processing as a feasible approach to utilize the biomass.