Nano-ZnO loaded nanoliposomes were prepared through thin layer hydration-sonication and heating methods and characterized by antimicrobial activity and physical property evaluations. The influence of lecithin: nano-ZnO ratio (5:1, 15:1, and 25:1 w/w) and the homogenization speed (5000 and 20,000 rpm) on the physical and antimicrobial properties of nanoliposomes were evaluated. Antimicrobial activities of nano-ZnO loaded nanoliposomes and free nano-ZnO were evaluated against some gram-positive bacteria (Staphylococcus aureus ATCC 25923, Bacillus ceruse ATCC 11778), gram-negative bacteria (Escherichia coli ATCC 2592, Pseudomonas aeruginosa ATCC 9027), and fungal strains (Aspergillus niger IBRC-M 30095, Botrytis cinerea IBRC-M 30162) by the determination of minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), and minimum fungicidal concentration (MFC). Well-dispersed ZnO nanoparticles in aqueous solutions were achieved by thin layer hydration-sonication and heating techniques. Moreover, MIC, MBC, and MFC values of nano-ZnO reduced, followed by encapsulation into nanoliposomes, significantly. The highest antimicrobial activity, encapsulation efficiency (85.9%), and absolute zeta potential (37.85 mV), as well as the smallest particle size (300.5 nm) and polydispersity index (0.21) of the nano-ZnO loaded nanoliposomes, were obtained by thin layer hydration-sonication technique at 20,000 rpm and with lecithin: nano-ZnO ratio of 25:1 (w/w) (p < 0.05).