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The environmental and economic benefits and burdens of including the first Short Cut Enhanced Nutrient Abatement (SCENA) into a real municipal wastewater treatment plant were evaluated using life cycle assessment (LCA) and life cycle cost (LCC). The implications of accomplishing nitrogen (N) removal and phosphorus (P) recovery via nitrite in the side stream were assessed taking into account the actual effluent quality improvement, the changes in the electricity and chemical consumption, NO, CO and CH emissions and the effects of land application of biosolids, among others. In addition, a case-specific estimation of the P availability when sludge is applied to land, therefore replacing conventional fertilizer, was performed. Furthermore, to account for the variability in input parameters, and to address the related uncertainties, Monte Carlo simulation was applied. The analysis revealed that SCENA in the side stream is an economic and environmentally friendly solution compared to the traditional plant layout with no side-stream treatment, thanks to the reduction of energy and chemical use for the removal of N and P, respectively. The uncertainty analysis proved the validity of the LCA results for global warming potential and impact categories related to the consumption of fossil-based electricity and chemicals, while robust conclusions could not be drawn on freshwater eutrophication and toxicity-related impact categories. Furthermore, three optimization scenarios were also evaluated proving that the performance of the WWTP can be further improved by, for instance, substituting gravitational for mechanical thickening of the sludge or changing the operational strategy to the chemically enhanced primary treatment, although this second alternative will increase the operational cost by 5%. Finally, the outcomes show that shifting P removal from chemical precipitation in the main line to biologically enhanced uptake in the side stream is key to reducing chemicals use, thus the operational cost, and increasing the environmental benefit of synthetic fertilizers replacement.