Slaughterhouse wastewater is characterized by high concentrations of organic matter. This creates a need to explore methods for its treatment before discharge. This study evaluated the efficiency of an integrated treatment process consisting of a laboratory-scale upflow anaerobic sludge blanket reactor and a pilot-scale horizontal subsurface flow wetland. This treatment was used for (i) the removal of organic matter through anaerobic–aerobic microbiological processes, (ii) the conversion of organic matter from hydraulic processes, and (iii) for bioremediation and phytoremediation. The treatment system was evaluated at hydraulic retention times (HRTs) of 7.5, 5.0, and 2.5 d; during the investigation, the influence of the HRTs on the removal efficiency of the system was evaluated. High efficiencies of 85% and 75% were obtained for COD_T and BOD, respectively, at an HRT of 7.5 d. The highest overall efficiency for the removal of total solids was observed at an HRT of 2.5 d. The results obtained confirm the feasibility of implementing the suggested system as an alternative for the adequate and sustainable treatment of slaughterhouse wastewater, and the system can be applied to slaughterhouses with similar conditions to those in this study.