The urgency to significantly reduce the impacts of climate change is felt around the globe. By signing the Paris agreement in 2016, 195 governments have agreed on a long-term goal of keeping the increase in global average temperature below 2 °C above preindustrial levels and on aiming to limit the increase to 1.5 °C. To reach these goals, major technological, organizational, and social changes in different sectors and their services are needed. To understand and steer the transition from the current energy system towards a carbon-free energy system, we propose a comprehensive engineering framework that integrates different aspects, such as technical, economic, cyber-physical, social, institutional and political, that are needed in the design of such a complex system. We explain the importance of combining different disciplines to provide comprehensive models and tools in order to support and achieve a sustainable, affordable, reliable and inclusive energy transition.