Rarefaction of fossil resources has led to a search of renewable carbon sources. One strategy consists on the development of optimized yeast strains for lipid production used as alternative source of biodiesel. These biotechnological approaches need the identification of key factors involved in the control of quantity and quality of storage lipids. Using genetic modification of Saccharomyces cerevisiae, heterologous expression of structural lipid body plant proteins, we obtained cell population presenting storage lipid overaccumulation. In a same culture, we observed cell to cell heterogeneity in lipid content due to the use of an inducible expression system. Because of this particularity, this strain appears as a powerful tool to evaluate the dynamic of lipid storage and carbon fluxes by measuring the biochemical changes (composition in lipids and carbohydrates) on single cells using the Synchrotron FTIR microspectroscopy.