Imaging native intracellular compartments in living cells is still challenging. The use of tagged proteins often modifies the morphology and the smooth running of the organelles. Methods based on intrinsic fluorescence of molecules upon excitation by deep-UV illumination are emerging for living cell imaging. We used deep UV light from synchrotron SOLEIL DISCO beamline to settle up and perform protein absorption imaging on single living yeasts. This technique was combined with transmission fluorescence microscopy. The visualization of contrasted signals inside the cells revealed chemical heterogeneity at the subcellular level. Fluorescence microscopy showed organelles with low fluorescence after 270-nm excitation. We could discriminate two populations, with high or low absorbance after 270-nm excitation. The first population was identified as lipid droplet using TMA-DPH and DPH lipid stains. Surprisingly, the second population corresponds to vacuoles. Combining deep UV fluorescence and absorption, two emerging techniques, enabled the acquisition of information on both organelle organization and chemical composition.