Clean and efficient alternatives for sustainable treatment of pig farming wastes are a priority in suburban areas located at High Mountain ecosystems. Among these technologies are anaerobic and aerobic digestion with added microorganisms (bioaugmentation) or nutrients (biostimulation) as biological activators. In a Colombian rural area located at 3000 m.a.s.l., focused on small-scale swine production, Bokashi fermentation with active dry yeast and some other composting methods were evaluated using two microbial inoculants and a sterile metabolic stimulant. In addition, these treatments were compared with a non-inoculated composting process used in the study area (control).This research shows that the biological additives improved the composting process performance and end product quality by shortening the degradation cycle, higher germination index, increasing nutrient content, and showing suppressive activity against Fusarium oxysporum. Nevertheless, Bokashi was the only treatment that decreased Enterobacteriaceae concentration below 1E+03 CFU g-1. Bokashi technology complies with Colombia’s environmental regulations for managing by-products from swine activities in critical ecological areas such as Forestry Protection Reserves in Highland ecosystems.