Maritime transport, pivotal to global trade, faces challenges in reducing greenhouse gas emissions. The International Maritime Organization aims to mitigate emissions through strategies like green marine fuels, with ammonia (NH3) emerging as a promising option. However, implementing ammonia bunkering (AB) in ports raises health, safety, security, and emergency (HSSE) concerns. This study addresses HSSE assessments and economic impact by examining AB’s implications for port sustainability, focusing on managing HSSE aspects to promote sustainable port practices and operational efficiency. The findings underscore the need for robust risk management, emergency preparedness, and collaboration to ensure safe and secure port operations amid the transition to cleaner energy sources. Findings from a case study of a planned green ammonia plant in Paldiski, Estonia, highlight potential economic and operational benefits, including driving sustainable growth, supporting AB’s port operations, and facilitating the maritime industry’s transition to cleaner energy through significant investment in port infrastructure. The research is based on empirical data from several projects on NH3 use in the maritime sector.