The decarbonization of maritime transport is a key objective in international shipping, with the sector targeting a 30% reduction in greenhouse gas (GHG) emissions by 2030. Estonia’s maritime sector must reduce emissions in line with European Union and International Maritime Organization (IMO) targets. However, selecting an optimal decarbonization pathway remains uncertain. This study applies a stakeholder-weighted Analytic Hierarchy Process (AHP) based on workshop discussions in which hydrogen, ammonia, methanol, dimethyl ether (DME), and biofuels were evaluated as potential marine fuels. Innovation Workshop on Maritime Decarbonization engaged around fifty stakeholders from Estonia’s maritime sector and beyond across three thematic areas: maritime digitalisation, sustainable ports, and shipping decarbonization. Stakeholders, including shipowners, ports, shipyards, fuel suppliers, and regulators, provided input on the suitability and feasibility of these fuels within the Estonian context. Repetition frequency and rated criticality were combined to calculate a normalised weighting structure across five key dimensions: infrastructure needs, technical readiness, economic viability, environmental performance, and operational safety. The findings indicate that, in Estonia, insufficient infrastructure and early-stage technological maturity constrain the near-term applicability of hydrogen, ammonia, and DME, while biofuels and methanol appear more compatible with existing systems. Although hydrogen and ammonia offer strong environmental benefits, their adoption is moderated by technical and logistical barriers. The study’s outcomes provide a foundation for future research and stakeholder collaboration, helping to raise awareness of overlooked decarbonization topics and inform subsequent initiatives within Estonia’s maritime sector.