The aim of this 5-year study was to evaluate the technical, economic, and environmental performances of a collective-based integrated treatment system for bioenergy production and nutrients removal to improve the utilization efficiency and reduce the environmental impact of land applied livestock manure. The study involved 12 livestock production units located in an intensive livestock area designated as nitrate vulnerable zone with large N surplus. The treatment system consisted of an anaerobic digestion unit, a solid–liquid separation system, and a biological N removal process. Atmospheric emissions and nutrient losses in water and soil were examined for the environmental assessment, while estimated crop removal and nutrient utilization efficiencies were used for the agronomic assessment. The integrated treatment system achieved 49% removal efficiency for total solids (TS), 40% for total Kjeldahl nitrogen (TKN), and 41% for total phosphorous (TP). A surplus of 58kWh/t of treated manure was achieved considering the electricity produced by the biogas plant and consumed by the treatment plant and during transportation of raw and treated manure. A profit of 1.61 €/t manure treated and an average reduction of global warming potential by 70% was also achieved. The acidification potential was reduced by almost 50%. The agronomic use of treated manure eliminated the TKN surplus and reduced the TP surplus by 94%. This collective integrated treatment system can be an environmentally and economically sustainable solution for farms to reduce N surplus in intensive livestock production areas.