This paper analyzes a moving grate biomass boiler operating with three alternative waste fuels, including biomass pellets, wood waste, and refuse-derived fuel (RDF) from a combination of thermal, economic, and environmental perspectives. The focus of this paper is on system functionality adaptation to retrofit the current systems operational conditions. A one-dimensional numerical bed model integrated with a black-box overbed model was developed to carefully investigate the fuel bed’s thermal characteristics, as well as the boiler’s output. According to the results, the system operates more efficiently under the biomass pellets feeding and annually generates 548 GJ heat, while it drops significantly in other scenarios. The system was economically evaluated based on a 25-year life cycle cost analysis. Subsequently, an internal rate of return (IRR) of 36% was calculated for biomass pellets, while the value reduced by 50% and 27% regarding wood waste and RDF, respectively. The fuel cost was identified as the main contributor to the total life cycle cost of the heating system, regardless of which feeding fuel was utilized. A long-term environmental impacts assessment of the boiler operation emerged, to show how plant-based fuels can significantly decrease the impacts of climate change that have originated from fossil fuel usage. The current study concludes that all the proposed scenarios are feasible to different degrees, and can extensively benefit a diverse set of energy sectors.