We use scanning-transmission X-ray microspectroscopy (STXM) for in situ characterization of the physicochemical changes in air-filled poly(vinyl alcohol) (PVA) based microbubbles upon soft X-ray irradiation. The microbubbles were illuminated directly in aqueous suspension with 520 eV X-rays and a continuous shrinkage of the particles with an illumination time/radiation dose was observed. Utilizing the intrinsic absorption properties of the species and the high spatial resolution of the STXM, the modifications of the particles' structure were simultaneously recognized. A thorough characterization of the microbubble volume, membrane thickness and absorption coefficient was performed by quantitative fitting of the radial transmittance profiles of the targeted microbubbles. Apart from the observed volume contraction, there was no significant change in the shell thickness. The chemical changes in the membranes were clarified via C K-edge near-edge X-ray absorption fine structure (NEXAFS) spectroscopy. It was revealed that the observed structural alterations go along with a continuous degradation of the PVA network associated with formation of carbonyl- and carboxyl-containing species as well as an increased content of unsaturated bonds.