Due to the increasing production of wastewater from human activities, the use of algal consortia for phytoremediation has become well‐established over the past decade. Understanding how interspecific interactions and cultivation modes (monocultures vs. polyculture) influence algal growth and behaviour is a cutting‐edge topic in both fundamental and applied science. Ammonium‐rich growth media were used to challenge the monocultures of Auxenochlorella protothecoides, Chlamydomonas reinhardtii and Tetradesmus obliquus, as well as their polyculture; NO3− was also used as the sole nitrogen chemical form in control cultures. The study primarily compared the growth, carbon and nitrogen metabolisms, and protein content of the green microalgae monocultures to those of their consortium. Overall, the cultivation mode significantly affected all the measured parameters. Notably, at 50 mM NH4+, the assimilation rates of carbon and nitrogen were at least twice as high as those in the monoculture counterparts, and the protein content was three times more abundant.Additionally, the consortium's response to NH4+ toxicity was investigated by observing a linear relationship between the indicator of tolerance to NH4+ nutrition and the N isotopic signature. The study highlighted a high degree of acclimation through metabolic flexibility and diversity, as well as species abundance plasticity in the consortium, resulting in a functional resilience that would otherwise have been unattainable by the respective monocultures.