Cobalt oxide nanoparticles are of great interest in recent years due to their potential applications. As very less work on synthesizing nanoparticles by microwave-assisted method, an attempt is made to synthesize cobalt oxide nanoparticles with zirconium doped at various weight % by the microwave-assisted method. The effect of doping on the Physico-chemical properties is reported. The result of P-XRD confirms the crystalline nature and the calculated average crystallite sizes were 12.29 nm, 11.95 nm, 11.06 nm, and 7.65 nm for 5, 10, 15, and 20 wt% of Zr doped Co3O4 nanoparticles respectively. The decrease in crystallite size is due to the occupation of the zirconium atoms at the vacant sites. The functional groups were identified by the FTIR spectrum. The UV-DRS spectra show the good optical transmission property of the samples and also indicate the decrease in bandgap with an increase in the concentrations of zirconium. The SEM pictures depict the morphological changes due to the agglomeration of zirconium particles. The SAED pattern in TEM images confirms the occupation of zirconium in cobalt oxide. The result of antibacterial activities indicates that the 20 wt% zirconium doped cobalt oxide nanoparticles display better activity.