Ship emissions cause serious environmental impacts and adverse effects toward human health. Therefore, the International Maritime Organization (IMO) restricted the fuel sulfur content (FSC) of marine fuels: FSC must be <0.5% m/m or <0.1% m/m in sulfur emission control areas, covering a range of fuels from distillate diesel-like fuels to low-sulfur heavy fuel oils (HFOs). As a result, ship emissions, e.g., sulfur oxides and particulate matter (PM) have been reduced. However, how FSC correlates with the toxicological potential of ship emissions is still uncertain. The objective of this study was to understand how the physical and chemical properties of particulate emissions from a marine engine operating on five marine fuels with different FSCs influence their toxicological outcome. For this scope, cytotoxic, genotoxic, mutagenic, and pro-inflammatory potentials of collected particles were evaluated in lung cell model systems. The involvement of intracellular reactive oxygen species and xenobiotic metabolism was also explored. While PM from different fuels’ combustion resulted in up to approximately 20% of reduction of cytotoxicity at the highest concentration, other toxicological outcomes, including clonogenic and genotoxic potentials, showed a stronger trend with the polycyclic aromatic hydrocarbon contents in PM compared with FSC. This trend was supported by evidence of a significant increase in gene mutation frequency and alterations in cellular mechanisms induced by an aromatic-rich HFO with an intermediate FSC. In conclusion, apart from reducing FSC in marine fuels, additional particle abatement systems should be considered to reduce the adverse effects of particulate emissions from shipping operations on human health.