Abstract Microalgae are photosynthetic microorganisms whose composition and biomass production can be influenced by manipulating the cultivation conditions employed. However, few studies have evaluated the effects of various cultivation conditions in autotrophic and mixotrophic conditions. The present work aimed to evaluate the effects of cultivation conditions on the cell growth and biosynthesis of fatty acids (FAs) by microalgae of the genus Chlorella in autotrophic and mixotrophic cultivation. Evaluation of the effects of the conditions was performed using an experimental design methodology. The highest values of maximum biomass concentration (Xmax) and maximum biomass productivity (Pmax) were obtained in autotrophic cultures. Palmitic acid was the FA obtained at the highest concentration in both cultivation modes. The concentrations of polyunsaturated FAs (PUFAs) ranged from 12.2 to 41.2% in autotrophic cultures and from 11 to 34.3% in the mixotrophic cultures. The variables photoperiod and sodium bicarbonate concentration showed the greatest influence on the Xmax, Pmax, and PUFA concentration in autotrophic and mixotrophic cultivations, respectively. This study verified that the selection of conditions and mode of cultivation contribute to the production of microalgal biomass and FA biosynthesis.