In this paper, attention is shifted from larger cities and regions to the important role of small municipalities in large-scale capacity waste management systems. The motivation of this analysis is to understand how small municipalities can be prepared for future inclusion in regional waste management. For the first time, solutions that include integrated treatment of municipal, agricultural, and industrial waste generated by small-scale municipalities are developed and assessed. For this purpose, five small Serbian municipalities with populations up to 30,000 inhabitants were chosen as case studies. The methodology integrates field data with material flow analysis (MFA) to analyze and evaluate future scenarios. A set of indicators which reflect the goals of waste management, including the total costs, was chosen for scenario comparison and evaluation. It was found that delivering generated waste to regional waste management centers can result in the most affordable environmental benefits for the representative municipalities. More advanced solutions, which include composting and joint treatment of municipal, agricultural, and industrial waste, can contribute to reaching waste management goals, but are more costly (217% and 652% comparing to delivering generated waste to regions). These results can be regarded as a representative for similar municipalities and can serve to support pre-planning decisions in other countries with problems in establishing regional waste management systems.