Adaptability, stealth, damage sustainability, extended range and reliability are key factors to every successful naval mission. The shipbuilding industry conceptualized and deployed a wide variety of power and propulsion architectures over the decades: from mechanical, to electrical and hybrid propulsion. The tendency towards increasingly complex propulsion and power generation systems calls for the development of intelligent control strategies, Energy Management Systems (EMSs), that can handle the complexity and exploit the increased degrees-of-freedom (DOFs) of hybrid systems, while conforming to all operational constraints. In current EMSs, the aim is to save fuel costs. However, the ability to adapt to a wide variety of missions in an ever changing world is important for naval vessels. Hence, this raises the question: Can further operational gains be achieved through the use of more sophisticated integrated control algorithm, with multiple optimization goals? The present work aims to address this issue, by developing such a control system for a naval platform. The proposed EMS can modulate shipboard energy production of a hybrid propulsion plant with hybrid power supply, considering the trade-off between multiple conflicting operating goals: fuel savings, maintenance costs of on-board assets, noise and infrared signature. A validated model of a Holland class Patrol Vessel has been utilized to test the proposed EMS. Simulation results under varying operational profiles demonstrate the applicability, validity and the advantages of the approach.