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Numerous experimental investigations conducted on different natural compounds; however, their effectiveness remains insufficient for overcoming the health problems. The effect of ozone on phytochemical characterization of propolis with its biological activities was investigated currently. HPLC showed that ozonized propolis (OP) contains several compounds with high concentrations like hesperetin, rosmarinic acid, coumaric acid, caffeic acid, and chlorogenic acid compared to non-ozonized propolis (NOP). Inhibition zones, killing kinetic time, MID and MBD indicated the effective role of OP against Salmonella typhi, Klebsiella pneumoniae, Bacillus subtilis, and Staphylococcus aureus besides Candida albicans compared to NOP. Low IC50 value (9.91 ± 1.25 μg/mL) was attributed to OP while NOP provide IC50 value 26.05 ± 0.50 μg/mL as antioxidant agent via DPPH. Inhibition of protein denaturation as a marker of anti-inflammatory was recorded for OP with IC50 value of 6.46 ± 0.66 μg/mL compared to the IC50 value of NOP (11.32 ± 1.33 μg/mL). Caco-2 cells line was inhibited with morphological changes by either OP or NOP, however OP reflected excellent IC50 9.9 ± 2.98 μg/mL contrast NOP (IC50 41.43 ± 0.62 μg/mL). Flow cytometric analysis of Caco-2 cells documented the apoptosis caused by propolis particularly NOP. The current study adopts a computational method to investigate the possible antibacterial and anticancer properties of rosmarinic acid and hespertin as main constituents of propolis. Rosmarinic acid and hespertin were docked as ligands against K. pneumonia (PDB ID: 6T77) and Caco2 cells (PDB ID: 1M17) receptors.