The energy sector is undeniably undergoing a critical period, faced with multiple challenges, whether economic, political or technological. These challenges are related to the requirements set on the sector to meet a wide range of social demands associated with the three traditional dimensions of a sustainable energy system, i.e., environmental sustainability, security of energy supply and economic sustainability. In particular, the environmental pillar has gained ground after the Paris Agreement, which has reinforced the requirement of a low-carbon transformation of the sector. A main challenge is to balance trade-offs among competing goals when designing energy and environmental policies. Although making the energy sector greener is a common aspiration of governments, and many countries are indeed being successful in this regard, the success comes at a price in terms of the other, non-environmental dimensions, of a sustainable energy system. The aim of this special issue is to look in detail on some of the most pressing environmental challenges faced by the energy sector as well as the trade-offs involved in reaching a greener energy system.