The energy efficiency and the environmental performance of ships are critical concerns for both the scientific and shipping communities. These aspects are strongly linked to the vessel’s operating profile. This study explores how variations in the ship’s operating profile and its level of detail affect the performance of a Capesize bulk carrier, focusing on fuel consumption, CO₂ emissions, and overall energy efficiency. A three-level simulation approach was applied using the vessel’s annual operating profile. The first level includes hourly simulations over one year, aiming at a more accurate performance assessment. The second focuses on a speed/power frequency analysis over the same period, while the third one uses noon or annual average speeds, considering both Laden and Ballast voyages. These multi-level simulations offer a comparative evaluation of the accuracy and relevance of each method. The study also examines the impact of operating profile variations, considering the installation of a shaft generator as an energy efficiency technology. Key results show that the hourly simulation closely matches real-life data, with a deviation of no more than 5%, whereas the average speed method shows deviations of 8–20%. Variations in the operating profile also influenced the shaft generator’s assessed benefit, ranging from 1.6 to 2.6%. The findings highlight the value of operating profile-based approaches in improving decision-making on fuel optimization and emissions reduction.