Complex biochemical mechanisms are being involved in oleaginous microorganisms during storage lipid and polysaccharide metabolism. Detailed biochemical analyses and monitoring of key enzymes involved in carbon metabolism were performed in Yarrowia lipolytica and Umbelopsis isabellina, which are often used as model oleaginous microorganisms. It was found that during the early oleaginous phase, the carbon source (glucose) was channeled to lipid accumulation, but also to polysaccharide biosynthesis. However, during transition from the early to the late oleaginous phase, glucose was exclusively converted to lipids, while in U. isabellina, but not in Y. lipolytica, an additional conversion of cellular polysaccharides into lipids was observed. After glucose depletion in the growth medium, cellular storage material was degraded either for generating maintenance energy or for supporting further microbial growth, depending on the availability of essential nutrients in the growth medium. We demonstrated that in both microorganisms, reserve lipids were exclusively used as an intra-cellular carbon source in order to generate energy for maintenance purpose. When cellular storage material degradation was related to new cell mass production, a bioconversion of lipids into new lipid-free material, consisting of polysaccharides and proteins, was observed in Y. lipolytica, while new lipid-free material in U. isabellina was richer in proteins. Lipid and polysaccharide remodeling may occur in some cases in both microorganisms. This study revealed some new biochemical features of oleaginous microorganisms that may be crucial for the design of new biotechnological processes, such as the production of bio-molecules of industrial, technological, and medical interest.