High-intensity ultrasound induces emulsification and cross-linking of protein molecules in aqueous medium. The stability and the functionality of the resultant protein-coated microbubbles are crucial in many of their applications. For example, the stability of drug-loaded microbubbles should be sufficiently long enough, in vivo, so that they can be ruptured only at specific sites for release of the drugs. In this study, we report the synthesis of stable and functional microbubbles, coated with chemically reduced lysozyme, using high-intensity ultrasound in aqueous solution. In the absence of chemical reduction, stable microbubbles were not produced with native lysozyme, indicating the importance of free -SH functional groups for protein cross-linking. The degree of cross-linking between lysozyme molecules was controlled by manipulating both the extent of chemical reduction of the intramolecular disulfide bonds and sonication time. The lysozyme-coated microbubbles are stable for several months and retain the enzymatic (antimicrobial) activity of lysozyme. The layer-by-layer (LbL) deposition of polyelectrolytes onto the protein-shell air-core template has been used as a versatile procedure to modify the surface properties of the microbubbles, indicating the possibility of adsorbing potential drugs and/orbiolabels on the surface of these microbubbles for therapeutic and diagnostic applications.