Microalgae cultivation is gaining interest as a sustainable alternative to the conventional wastewater (WW) treatment and nutrient recovery. Current study presents a comprehensive life cycle assessment (LCA) of microalgae cultivation in distinct wastewaters. Two different microalgae species in three different wastewaters were compared for sustainability performance in six scenarios. LCA was conducted using SimaPro (v9.3.0.3) and ReCiPe 2016 Midpoint method. The findings of the study reveal that global warming potential ranged between −678 and − 1357 g CO2eq./m3. Chlorella sp. cultivated in dairy WW shown higher environmental performance across the scenarios with GWP of −1357 g CO2eq./m3. The average global warming potential (GWP) of single-pot microalgae-based wastewater treatment got reduced by 240 %. The key inference of this study is that cultivation of the microalgae as single-pot treatment system not only helps in environmental sustainability but also holds significant promise for combating climate change as negative emission technology (NET).