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Background Organic acids like succinic and citric acids are of great interest as platform organic products that play important roles as precursors for a wide range of bio-based materials. Succinic and citric acids can be successfully produced biotechnologically from renewable resources of both hydrophilic and hydrophobic nature through efficient microbiological conversion. Yarrowia lipolytica represents one of the most versatile microbial factories in terms of organic acids production, as it easily develops and produced metabolites starting from glucidic-based and/or lipid-based substrates. Results The purpose of this work was to investigate the ability of Y. lipolytica to adapt to hydrophilic and hydrophobic sources and to biosynthesize important platform chemicals like succinic and citric acids. The selected strain was monitored during a batch cultivation for 192 h on 100 g/L carbon source: pure glycerol as a hydrophilic source, sunflower waste cooking oil as a hydrophobic source, and crude glycerol deriving from biodiesel production as a mixture of hydrophilic and hydrophobic sources. Cellular viability, biomass accumulation, and metabolites formation in terms of succinic acid and citric acid was monitored, and the highest results were registered for cultivations performed on waste cooking oil [10.35 ± 0.29 (log10) CFU/mL, 8.15 g/L cell dry weight, 3.50 ± 0.04 g/L citric acid, and 21 ± 0.16 g/L succinic acid]. Conclusion The results obtained in this work outline the industrial potential of the oleaginous yeast strain of Y. lipolytica to bioconvert lipidic residual biomass into valuable organic compounds with wide-range applicability.