Currently there is an energy transition from fossil fuels towards zero emission fuels within the marine sector. In addition to this, improvements are made in system design with regard to standardization of which allows for variation. The combination of these two improvements is found in the EU H2020 NAVAIS project which focuses on customer tailored vessels in combination with a standardized and modularized approach. The specific objective is to use modularity to help support the development of zero-emission propulsion methods for a ferry. The objective is fulfilled by answering the main question of this research: “How can the energy carrier and conversion system of a ferry be made environmentally friendly and modular and how does the inclusion of low emission and modularity objectives impact the power supply and total design of the ferry?” In the approach a Systems Engineering approach is used, including the V-cycle or the RFLP approach. In this approach the design is approached by the elaboration of the Requirements, Functionalities, Logical design and the Physical design. Based on the main vessel requirements, research requirements are defined as well which are the system’s ability to be: future proof, modular, fulfilling the energy and power requirements, the ability to be refitted and technical feasible. A platform approach is defined, which is called a platform approach, and for this research includes: The top-down approach, the common-core approach the design approaches combined in the platform approach are practically applied by using a design support tool which is the Design Structure Matrix. The DSM and specifically the clustering algorithm has the goal to find modules based on minimizing interactions between modules. This is done based on the logical or technical decomposition where only the sub-systems are included in the matrix. The interactions between the sub-systems are defined using a binary definition. The clustering algorithm is used where random groups of sub-systems, named clusters or potential modules, are formed which then are evaluated based on the interactions and parameters to control the size and interactions between the clusters. Simulated annealing is used to optimize the solutions in combination of multiple runs for the defined system configurations. In this way interchangeable modules can be defined which can be used for the diesel generator, dual fuel and fuel cell configuration. The multiple solutions are merged into combined potential modules after which the results are evaluated. The evaluation is done based on the number of interactions, the technical feasibility and physical evaluation of the modules and finally based on the ability to standardize the interactions of the module. These steps result in a suggestion of modules which are interchangeable and are based on a minimization of interactions between or outside the modules. While leaving the ability to extend the method to allow for new alternative fuel systems.