The International Maritime Organisation focuses on decarbonising the operational phase of a ship's life cycle. However, shipbuilding contributes to a significant amount of greenhouse gas emissions and air pollutants and has negative impacts on society. Holistic and transdisciplinary studies of the shipbuilding energy sector are lacking and a holistic approach is needed to discuss the potential of measures and tools to improve the shipbuilding industry with zero emissions. This study is an interdisciplinary approach to provide trends, recommendations and policies for decarbonisation of the shipping industry from a life cycle perspective. Taking into account a holistic and transdisciplinary approach, the energy sector in shipbuilding is categorised into an energy supply system, an energy economic system and an energy ecosystem, and the main disciplines for improving energy efficiency and promoting “zero emissions” for shipyards are identified, measures and tools within each discipline are proposed, and their mitigation potential and key issues for improving energy efficiency and reducing air emissions from shipyard activities are discussed. The case study highlights the economic, environmental and sustainability benefits of implementing the proposed modern energy system in an Italian shipyard. Although there is no silver bullet to eliminate air emissions in the shipbuilding industry due to the complexity, the different reduction potentials, the costs and the relationship and interaction between measures and tools, the implementation of the energy management framework can accelerate the transition to a zero-emission shipbuilding industry.