A significant proportion of global carbon dioxide emissions are attributed to ocean-sailing ships and shipping emissions are predicted to double in less than 30 years. This paper investigates the benefit of using weather ship routing optimisation, assessing the ship emissions for minimum distance routes and optimised routes. The present contribution merges the estimation of shipping pollutants and their mitigation through weather routing optimisation; two lines of research widely analysed separately but seldom discussed together. A previously developed open software of weather ship routing is used to obtain the minimum cost (i.e. optimised route) in terms of sailing time, using high-resolution wave forecasting. The assessment of fuel consumption and ship emissions calculations were inspired by the STEAM2 bottom-up approach, in conjunction with the estimation of the power increase needed to overcome speed decrement due to waves. Several scenarios covering the Western Mediterranean Short Sea Shipping routes (from 24 to 600 nautical miles and using a real Ro-Pax vessel) are compared in terms of emissions between the minimum distance route and the optimum. The ship routing optimisation reveals a reduction up to 30% of ship emissions during severe storms on longer routes. Nevertheless, all the cases studied show emissions mitigation when ship routing optimisation is used. The expected increase of extreme weather events, in terms of frequency, intensity and duration due to climate change, suggests a gradual gain of implementing weather ship routing optimisation in all types of routes, regardless of the distance.