Energy systems in cities need to be decarbonized and are becoming more integrated via energy sector coupling. Today, cities often use simple methods to assess their low carbon targets, e.g., carbon calculators, and these methods use annualized carbon reduction potentials. For example, reductions from heat savings in buildings or fuel demand in transport. This is done because it is simple and fast. This paper describes a methodology that goes beyond carbon calculators and assesses highly renewable energy systems. The methodology is carried out for a case city—Sønderborg, Denmark. Using a national 100% renewable energy study and a suitable energy system analysis tool (EnergyPLAN), the method accounts for inter-sector coupling and energy system dynamics. The energy system is assessed by comparing the results from the analysis tool against numerous key sustainability factors for a Smart Energy System. The paper illustrates how the method delivers a sustainable 100% renewable Smart Energy System for Sønderborg, which can be part of the Danish energy system in 2050 based on local resources. The paper discusses the broader applicability of the method within strategic energy planning.