Sustainability assessment of a waste management system is a very complex problem for numerous reasons. Firstly, it is a problem of environmental assessment, economic viability and social acceptability, and also a choice of the most practical waste treatment technique, taking into account all the specific areas in which a waste management system is implemented. For these reasons, among others, it is very important to benchmark, cooperate and exchange experiences in areas with similar characteristics. In this study, a comparison of waste management scenarios in the Cities of Niš and Sofia was performed. Based on the amount and composition of municipal solid waste, and taking into account local specifics (economic conditions, social acceptance, etc.), different scenarios were developed: landfilling without energy recovery, landfilling with energy recovery, mechanical-biological treatment, anaerobic digestion with biogas utilization and incineration with energy recovery. Scenario ranking was done using multi-criteria analysis and 12 indicators were chosen as the criteria. The obtained results show that the most sustainable scenario in both case studies is the mechanical-biological treatment (recycling, composting and Refuse Derived Fuel production). Having in mind that this scenario is the current waste management system in Sofia, these results can help decision-makers in the City of Niš in choosing a successful and sustainable waste management system.