The ultrasound-assisted self-assembly and cross-linking of lysozyme at the water–air and water–perfluorohexane interfaces are shown to produce lysozyme-shelled hollow microbubbles (LSMBs) and microcapsules (LSMC), respectively. The arrangement of lysozyme at the air–liquid or oil–liquid interfaces is accompanied by changes in the bioactivity and conformational state of the protein. The interaction of LSMB and LSMC with human breast adenocarcinoma cells (SKBR3) is studied. LSMB and LSMC are phagocyted by cells within 2 h without exerting a cytotoxic activity. The cellular internalization kinetics of LSMB and LSMC and the effects on cell cycle are evaluated using flow cytometry. Evidence for the internalization of microparticles and degradation within the cell are also monitored by confocal and scanning electron microscopic analyses. The integrity of cell membrane and cell cycle is not affected by LSMBs and LSMCs uptake. These studies show that the positively charged LSMB and LSMC are not cytotoxic and can be readily internalized and degraded by the SKBR3 cells. LSMBs and LSMCs show a different uptake kinetics and intracellular degradation pattern due to differences in the arrangement of the protein at the air–liquid or oil–liquid interfaces.