Collecting urban solid waste (USW) is a critical and essential phase for proper waste management and valorization. To date, many data are available for large cities, but few studies have focused on low-density areas, such as mountainous regions. Considering this lack in the literature, this study aimed to compare two separate waste collection systems in two mountainous valleys in terms of effectiveness and GHG emissions. In the first scenario, a mixed collection system (door-to-door + centers) was used, while in the other, waste was separately collected by a full door-to-door system. The results suggested that the full door-to-door system achieved better performance than the mixed collection system (door-to-door + centers), with a fraction of separate waste collection compared to the unit equals (0.84 ± 0.01 vs. 0.79 ± 0.02). Moreover, the full door-to-door system represented the best option for collecting separate waste in mountainous areas in terms of GHG emissions, with 11.21 kgCO2, eq twaste−1 emitted vs. 15.62 kgCO2, eq twaste−1 in the case of the mixed system. Despite utilities emitting a higher amount of GHGs in the door-to-door scenario (4.66 kgCO2, eq inh−1 y−1), they were fully compensated for by the low GHG emissions from citizens in the mixed scenario (1.77 kgCO2, eq inh−1 y−1 vs. 6.65 kgCO2, eq inh−1 y−1). Given the low amount of data on this topic, this work could be considered as a pioneer study of waste management in mountainous areas by comparing the results of two systems regarding effectiveness and GHG emissions. The outcomes of this study could be helpful for waste utilities, institutional agencies, and local communities and also serve as a tool for decision-making in the case of comparing the different options for USW collection systems.