Marine vessels execute many missions during their life cycle, each associated with a different required power profile. The required power is to be provided by the power plant, which has a fixed set of equipment such as diesel engines, generator sets, electric machines, and batteries. Typically, the control of vessel's power plants consist of two levels; a primary level with local controllers for the power plant components, and a secondary level that determines the distribution of the required power to the various components in the power plant. The state-of-the-art only considers a multi-level power plant control architecture assuming a fixed power plant layout, but in practice, the fixed power plant layout may not suffice for generating the power demand dictated by a new mission. This may lead to inefficient use of components, risk of overloading components, or the inability to deliver the required power. To handle this issue, equipment modifications such as additions, removals or replacements would probably be necessary, along with modifications in the multi-level control scheme. To enable the seamless operation of the multi-level plant control system after the modifications is essential for guaranteeing safety and reducing the downtime, which could be achieved by a control architecture that allows for modular use of the power plant components. This thesis presents the design methodology of a mission-oriented modular control system for marine power plants. To this end, first power profiles, power plant layouts and control systems of multiple vessels such as tugboats, offshore support vessels, cargo ships and cruise ships are analyzed. By decomposing the power profile in two components, the propulsion and auxiliary power demand, the correlation between the power profile of a vessel and its mission is derived, and an algorithm that computes the power profile using mission and vessel data is proposed. Furthermore, the correlation between the power profile and the layout of the power plant is also investigated, with emphasis on how changes in the power profile result in power plant automation modifications. A modular secondary control level is then designed to cope with the required power plant automation modifications, by combining the Equivalent Consumption Minimization Strategy (ECMS) with Supervisory Switching Control (SSC). In this thesis we consider battery modifications, following the example of Wärtsilä's ZESPacks. Simulation results are used to show the performance of the proposed switching control methodology, in relation to the stability of the components in the power plant after automation modifications occur. The main contribution of this thesis is the novel approach for the secondary level power plant control system, introducing modularity to the otherwise assumed fixed layout of the power plant. Furthermore, the proposed algorithm can be used to determine the expected power profile for a new mission, to identify required modifications of the power plant equipment.