Environmental considerations, concerning the negative impacts of ship exhaust gases and particles on ambient air quality, are behind the requirements of cleaner marine fuels currently applied in designated emission control areas (ECAs). We investigated the impact of a ship operating on two types of fuel on the indoor air quality onboard. Gaseous and particulate air pollutants were measured in the engine room and the accommodation sections on-board an icebreaker operating first on Heavy Fuel Oil (HFO, 1%-S), and later Marine Diesel Oil (MDO, 0.1%-S). Statistically significant decrease of SO2, NOx, PM2.5 and particle number concentration were observed when the ship was operating on MDO. Due to the higher content of alkylated PAHs in MDO compared to HFO, the concentration of PAHs increased during operation on MDO. The particulate PAHs classified as carcinogens, were similar to or lower in the MDO campaign. Chemical analysis of PM2.5 revealed that the particles consisted mainly of organic carbon and sulfate, although the fraction of metals was quite large in particles from the engine room. Principal Component Analysis of all measured parameters showed a clear difference between HFO and MDO fuel on the indoor environmental quality on-board the ship. This empirical study poses a first example on how environmental policy-making impacts not only the primary target at a global level, but also brings unexpected localized benefits at workplace level. The study emphasizes the need of further investigations on the impact of new marine fuels and technologies on the indoor air environments on board.