Liposomes were modified using two different methods. In Method 1, liposomes were modified by mixing whole lysosomal proteins, lipid, and cholesterol before preparation. For Method 2, the liposomes were modified by mixing whole lysosomal proteins after liposome preparation. Method 1-modified liposomes exhibited improved cell mortality compared to Method 2-modified liposomes. The modified liposomes were then evaluated for their antimicrobial activity against lysosomal enzymes, and Escherichia coli did not modify the liposome surface. The whole lysosomal membrane proteins extracted from the lysosomes in Saccharomyces cerevisiae were analyzed using two-dimensional electrophoresis to find specific proteins associated with antimicrobial activity and to construct recombinant S. cerevisiae proteins. Additionally, genes related to antimicrobial activity were identified, and the liposomes modified by lysosomal membrane proteins of recombinant S. cerevisiae tagged with green fluorescence proteins were prepared and overexpressed. The modified liposomes exhibited improved antimicrobial activity with an almost two-fold increase in the cell mortality rate, suggesting crucial roles as potential therapeutics.