The exogenous addition of synthetic phytohormones such as auxins, cytokinins, and gibberellins, among others, to the culture of microalgae under abiotic stress is a strategy to increase cell density and content although this effect is dependent on the concentration used, supplementation time, and growth stage when it is supplied. Mutualistic interaction of microalgae with Azospirillum brasilense a plant growth-promoting bacterium, improves physiology and the biotechnological processes based on microalgae, due to the ability of A. brasilense to produce several phytohormones as cytokinins, gibberellins, jasmonic acid, brassinosteroids, and auxins, mainly indole-3-acetic acid (IAA). Therefore, this study analyzed the effect of A. brasilense on Chlorella vulgaris and Tetradesmus (Scenedesmus) obliquus cultured under different concentrations of nitrogen limitation to increase cell density and compound accumulation simultaneously and compare it with the effect of the exogenous supplementation of synthetic IAA. Moreover, the effect of this stressful condition on tryptophan (Trp) and IAA production by microalgae and A. brasilense, respectively, was also evaluated during their synergic interaction. The results of this study demonstrated that under nitrogen stress A. brasilense induced an increase on cell density and compound accumulation simultaneously, mainly carbohydrates and proteins, in both microalgae evaluated. This result highlights that under this stressful condition, the combined effects of the several phytohormones produced by A. brasilense on microalgal physiology overcame the effect of synthetic IAA acting independently.