The transportation industry has been scrutinized for its contribution towards the global greenhouse gas emissions over the years. While the automotive sector has been regulated by strict emission legislation globally, the emissions from marine transportation have been largely neglected. However, during the past decade, the international maritime organization focused on ways to lower the emission intensity of the marine sector by introducing several legislations. This sets limits on the emissions of different oxides of carbon, nitrogen and sulphur, which are emitted in large amounts from heavy fuel oil (HFO) combustion (the primary fuel for the marine sector). A 40% and 70% reduction per transport work compared to the levels of 2008 is set as target for CO2 emission for 2030 and 2050, respectively. To meet these targets, commonly, methanol, as a low-carbon fuel, and ammonia, as a zero-carbon fuel, are considered. But for the well-being of the marine ecosystem, nitrogen and sulphur oxides, emitted from ammonia combustion, are more harmful due to their acidification and eutrophication impacts. Thus, the evaluation of the emission impact and the production cost must be done for the different production pathways of both fuels to estimate the most efficient way for a sustainable transition of marine transportation. Therefore, in this study, a well-to-wake enviromental and techno-economic analysis of methanol and ammonia is done to evaluate the most feasible pathway to meet those targets. Results show that, despite methanol’s carbon-based fuel nature, it is a more sustainable option for the shipping sector in terms of meeting the emission reduction targets as well as having a lower impact on the hydrosphere.