The coffee processing wastewater (CPWW) requires treatment before being disposed of in the environment or reused due to its high organic and inorganic composition and a low pH. The indigenous microbiota from CPWW is highly diverse and could be selected as inoculums in treatment waste plants. Considering the physico-chemical characteristics of wastewater coffee, we elaborate on steps to select the microbial consortium that showed positive impact via decreasing the pollutant parameters of this effluent. The effectiveness was confirmed using wastewater from different origins with different chemical characteristics. A bacterial consortium composed by Serratia marcescens CCMA 1010 and CCMA 1012, Corynebacterium flavescens CCMA 1006, and Acetobacter indonesiensis CCMA 1002 was selected as the inoculums-based phenotypic assays. The mixed inoculum showed a highly active population (11.18 log CFU mL−1), promoting an 85% decrease in biochemical oxygen demand and a 60% decrease in chemical oxygen demand. There was also an 80% reduction in phosphorus and nitrogen. The final pH changed from 6.0 to 7.5. Additionally, the eco-toxicity using Daphnia similis was reduced by more than 59%. The microbial inoculum was efficient in the biological treatment in CPWWs, demonstrating the efficiency and robustness of the selected strains, independent of the physico-chemical characteristics of wastewater.