The study’s objective is to create a method to select the best course of maintenance action for each state of ship propulsion system degradation while considering both the present and future costs and associated carbon intensity indicator, CII, rates. The method considers the effects of wind and wave action when considering fouling and ageing. The ship resistance in calm, wave, and wind conditions has been defined using standard operating models, which have also been used to estimate the required engine power, service speed, fuel consumption, generated CO2, CII, and subsequent maintenance costs. The maintenance takes into consideration the effects of profit loss because of lost opportunities and efficiency over time. Any maintenance choice has total costs associated with it, including extra fuel, upkeep, and missed opportunities. Using a discrete-time Markov chain, the ship’s propulsion system maintenance schedule is optimized. A decision has been reached regarding the specific maintenance measures to be undertaken for each state of the Markov chain among various alternatives. The choice of optimal maintenance is related to a Markov decision process and is made by considering both the current and future costs. The developed method can forecast the propulsion system’s future states and any required maintenance activities.