Lysosomes, as a cell organelle type, are safe biological control agents that may be possible replacements for chemical antimicrobial agents because they are simply isolated from egg white. In this study, it was found that the lysosomes isolated from egg white exhibited pH-dependent antimicrobial activity, with the optimal activity found at pH 6.0. The efficiency of lysosomes in inhibiting bacterial growth and activity was evaluated over a 12-h treatment period. Seven different microorganisms were used as bacterial strains, and the lysosomes showed a significant antimicrobial effect against all strains. In addition, the antimicrobial activity was maintained for 100 days, and there did not appear to be any resistance of E. coli to the lysosomal activity up to the eighth culture. However, the lysosomes did not affect the viability of mammalian cells, suggesting the biocompatibility of lysosomes. These highly effective lysosomes have a bright future in the application of novel antimicrobial sources as a cell organelle type.