In the context of growing concerns about power disruptions, grid reliability and the need for decarbonization, this study evaluates a broad range of clean technologies to replace traditional emergency diesel generators. A scenario-based stochastic optimization framework using actual load profiles and outage probabilities is proposed to assess the most promising options from a pool of 27 technologies. This framework allows a comparison of costeffectiveness and environmental impact of individual technologies and combined backup power systems (BPS) across various scenarios. The results highlight the trade-off between total annual system cost and emissions. Significant emission reductions can be achieved at moderate cost increases but deep decarbonization levels incur higher costs. Primary and secondary batteries are included in optimal clean fuel-based systems across all decarbonization levels, combining cost-effective power delivery and long-term storage benefits. The findings highlight the often-overlooked importance of fuel replacement on both emissions and costs. Among the assessed technologies, ammonia generators and hydrogen fuel cells combined with secondary iron-air batteries emerge as cost-effective solutions for achieving decarbonization goals. To ensure a broad range of applicability, the study outlines the impact of emergency fuel purchases, varying demand patterns and demand response options on the optimal BPS. The research findings are valuable for optimizing decisions on clean BPS to economically address diverse applications and decarbonization targets.