In most organisms, storage lipids are packaged into specialized structures called lipid bodies. They contain a core of storage neutral lipids surrounded by a monolayer of phospholipids, and numerous proteins which vary strongly according to the species. In particular, structural hydrophobic proteins stabilize the interface between lipid core and cellular aqueous environment (PAT proteins, apolipoproteins, oleosins). We developed a genetic approach using Saccharomyces cerevisiae to obtain heterologous expression of Arabidopsis thaliana lipid body proteins: oleosin AtOle1 or caleosin AtClo1. These transformed yeasts overaccumulated lipid bodies, leading to a specific increase in storage lipids. Exploration of these cells using single cells FT-IR microspectroscopy was done to understand the dynamics of lipid storage and carbon fluxes by measuring the changes of spectral fingerprints of biological macromolecules. Statistical analysis of data shows a clear effect on carbohydrate pool and more precisely, we measured a decrease of glycogen in our modified strains. These observations were confirmed using biochemical quantification of storage carbohydrates, glycogen and trehalose. Our results demonstrated that neutral lipid and storage carbohydrate fluxes were tightly connected and co-regulated.