The aim of the study was to obtain vitamin B12-enriched biomass of non-conventional yeast Yarrowia lipolytica A-101. The cultivations were performed on waste from biofuel production in aerobic conditions at different temperatures (20–30 °C) and pH values (4.0–7.0) of the medium, with and without the addition of cobalt, l-methionine, molybdenum, δ-aminolevulinic acid, and niacin. A temperature of 30 °C and pH between 5 and 6 were the optimal conditions for obtaining B12-enriched yeast biomass on biofuel waste. In such conditions, Y. lipolytica A-101 contained 9 µg of vitamin B12 per 100 g of dried biomass. The addition of the ingredients mentioned above to the medium did not exert a significant effect on the B12 concentration. Y. lipolytica are able to accumulate this vitamin from the medium in a similar manner to animal cells. Additionally, it should be noted that the dried biomass of Y. lipolytica appeared to be safe for consumption. Taken together, these data showed that Y. lipolytica can be used as a nutritional supplement to increase the intake of vitamin B12, especially at risk of vitamin B12 deficiency.