Europe’s waterborne transport is a significant contributor to greenhouse gas (GHG) emissions, accounting for approximately 13% of overall transport emissions. Thus, meeting ambitious climate targets is imperative and requires accelerating the transition to sustainable, climate-neutral fuels in this sector. However, the adoption of sustainable alternative fuels (SAFs) is often slow due to concerns around safety, global availability, technological maturity, and economic viability. SAFeCRAFT seeks to address these challenges by leveraging the ZEWT Partnership’s existing network of stakeholders and infrastructure to develop, validate, and demonstrate SAFs on board oceangoing vessels. This includes fuel distribution, bunkering, storage, handling and supply, power conversion, and possible residue handling. This study employs the Quality Function Deployment (QFD) methodology to systematically evaluate key performance indicators (KPIs) influencing the adoption of alternative fuels, including liquid hydrogen (LH2), compressed gaseous hydrogen (CGH2), liquid organic hydrogen carriers (LOHCs), and ammonia (NH3). To address these KPIs, functional features are established and prioritized. This study provides a structured, QFD-based framework to facilitate the maritime sector’s transition to sustainable fuels, offering valuable insights for policymakers and industry stakeholders to align technological advancements with regulatory and economic considerations, ultimately supporting the European Commission’s 2040 emissions reduction targets.