The properties of nanoparticles have been used in a wide range of potential applications in food industry, medicine, microbial biotechnology, cosmetics, environmental production. Research results of evaluation of the effect of Fe₃O₄ and TiO₂ nanoparticles applicated in large concentration limits on some parameters of pigmented yeast strain Rhodotorula gracilis CNMN-Y-30 are presented in this paper. It was established that nanoparticles selected for study caused toxic effects on β-caroten accumulation and activity of antioxidant enzyme catalase depending on concentration and nanostructure. The strong correlation between concentration of nanoparticles and evaluated components has been revealed at studied yeast strain. Coefficients of correlation varied in limits R² = 0.623... 0.951. For the first time, the determination of β-carotene accumulation and catalase activity rate as functional tests for estimation of toxicity of nanoparticles for pigmented yeast strain Rhodotorula gracilis was effectuated. Thus, it was established that adaptive response of yeast strain to the presence of Fe₃O₄ and TiO₂ nanoparticles has been manifested by modification of the processes of β-carotene biosythesis and catalase activity.