Three strains of the freshwater microalgae used for wastewater treatment, Chlorella vulgaris and Chlorella sorokiniana co-immobilized separately in alginate beads with the microalgae-growth-promoting bacterium Azospirillum brasilense Cd, resulted in significant changes in microalgal-population size, cell size, cell cytology, pigment, lipid content, and the variety of fatty acids produced in comparison with microalgae immobilized in alginate without the bacterium. Cells of C. vulgaris UTEX 2714 did not change in size, but the population size within the beads significantly increased. On the other hand, C. vulgaris UTEX 395 cells grew 62% larger, but their numbers did not increase. The population of C. sorokiniana UTEX 1602 increased, but not their cell size. The content of pigments chlorophyll a and b, lutein, and violoaxanthin increased in all microalgal species. The lipid content also significantly increased in all three strains, and the number of different fatty acids in the microalgae increased from four to eight. This study indicates that the microalgae-growth-promoting bacterium induced significant changes in the metabolism of the microalgae.