The maritime industry is facing increasing pressure to reduce greenhouse gas (GHG) emissions and transition towards sustainable fuel alternatives. This study addresses the need for a comprehensive classification of fuels based on a comparative analysis, considering multiple criteria of interest to stakeholders. Utilizing the entropy method, the relative weights of eight criteria for four fuel alternatives are identified, highlighting the significance of factors such as CO2 emissions, fuel cost, necessary investments, social acceptance, and technological maturity. The multi-criterion decision-making method PROMETHEE II is then employed to rank the alternatives, providing valuable insights for the decarbonization of supply chain operations. The findings underscore the critical importance of environmental considerations, social responsibility, and technological maturity in fuel selection for the maritime industry. This research contributes to the industry’s efforts to achieve climate neutrality and align with stringent environmental regulations. The proposed framework offers a holistic perspective that prioritizes the interests of all stakeholders, fostering sustainable maritime transportation and guiding strategic decision-making for policymakers and industry stakeholders.