Abstract The international shipping industry transports about 90 per cent of the global trade volume and is responsible for only two per cent of the anthropogenic carbon dioxide emissions. Consequently, the shipping sector is considered as an environmentally friendly transport mode. Nevertheless, global shipping can also improve its environmental footprint. So that in recent years clean shipping initiatives have been placed on the political agenda with the implementation of the Sulphur Emission Control Area (SECA) and Nitrogen Emission Control Area (ECA) regulations and the Global Cap. The next target of the International Maritime Organisation (IMO) in the sequel of the Paris Agreement of climate protection is dedicated to reduction of the Greenhouse Gas (GHG) emissions by up to 50 % until the year 2050. The paper investigates and discusses the research questions to what extent ammonia can be used in Baltic Sea Region (BSR) to propel merchant vessels and how ammonia can fulfil future demands under technical, economic and infrastructural aspects to become the green fuel for the Baltic Sea Region (BSR) shipping industry. The study benchmarks the properties of ammonia as marine fuel against Marine Gas Oil (MGO) and Liquified Natural Gas (LNG). The research is based on secondary data analysis that is complemented by expert interviews and case studies, and the results are empirically validated by data that were collected during the EU projects “EnviSuM”, “GoLNG”, “CSHIPP” and “Connect2SmallPorts” that took place within the last four years in the BSR.