The transition towards renewable energy will operate on different geographical scales. Many of the concrete steps will address the local level; however, these have to align with the broader energy perspective. It is therefore necessary to develop methods to enable cities to assess if their strategies are compatible with the surrounding energy systems. This paper presents a methodology to design Smart Energy Cities within the context of 100% renewable energy at a national level. Cities and municipalities should act locally what concerns local demands, but acknowledge the national context when addressing resources, industry and transport. The method is applied to the case of transitioning the municipality of Aalborg to a 100% renewable Smart Energy System within the context of a Danish and European energy system. The case demonstrates how it is possible to transition to a Smart Energy City that fits within a 100% renewable energy context of Denmark and Europe.