The growing population and the consequent protein scarcity have led to innovation in proteinaceous feed production methods. In this regard, the upcycling of nitrogen rich effluents into microbial protein (MP)/single cell protein (SCP) is considered as an innovative solution. This paper aims to employ life cycle assessment to identify the most environmentally friendly strategy to upcycle nitrogen (N) and carbon (C) flows from wastewater treatment plant (WWTP) into MP. Accordingly, several pathways for integrating WWTP and MP production facility were evaluated, in terms of C source (i.e., biogas or biomethane) and the pretreatment method applied to the reject water (RW) (i.e., centrifugation + filtration + pasteurization, electrochemical extraction, bio-electrochemical extraction). The results indicated that electrochemical and bio-electrochemical N recovery not only safely extracted N from RW but also led to promising solution for MP production from WWTP effluents. The pathway including bio-electrochemical N recovery and use of biologically upgraded biogas for MP had 42.17%, 195.95%, and 172.03% better environmental performance regarding human health, ecosystem quality, and resource scarcity, respectively, compared with standalone WWTP without MP production. However, the electrochemical N recovery outperformed other scenarios in the human health damage category with a net impact of 2.72 DALY/FU and in ecosystem quality damage category with a saving of −0.033 Species/FU. The results reported herein indicated that the use of chemical nutrients to enrich the cultivation medium had significant impacts on the overall environmental performance of the suggested biorefinery. Decreasing the consumption of synthetic nutrients and improving N to protein conversion efficiency by 20% can make the established pathway much more competitive with conventional proteinaceous feed sources such as soybean meal.