Abstract In this paper, the authors present an innovative approach to compare the most promising innovative technologies for energy production and storage for maritime applications. The developed algorithm, which include a large database built with market and literature data, compares several possible solutions, including innovative ones, from the environmental, economic and energetic standpoints. A detailed decription of the functions implemented in the database is reported, explaining also in detail the algorithm developed to evaluate and compare the technologies. Then, the methodology is applied to two case studies to demonstrate the algorithm’s potential, the reliability of the wide range of data included in the database and the impact of the scenario on the final results. The investigated case studies are: (i) a small size passenger ship operating in urban areas (ii) a large size cruise ship. Analyzing the first case study, a focus on the impact of generation unit and fuel storage systems is developed for the most promising solutions, represented by fuel cells in comparison to standard solutions. The second case study shows that, as could be expected, the most promising solutions in this range of application is the use of MDO or LNG in Internal Combustion Engines. In order to evaluate the future potential of the different alternative fuels, a sensitivity analysis is performed to evaluate the impact of the increasing emissions' importance: methanol, LNG, and ammonia are indicated as the most futurible fuels. It is worth noting that the presented approach has a general validity, thus it can be applied to other ships' typologies; the modular structure also allows for including further emerging technologies.