The green synthesis of metal oxide nanoparticles is an efficient, simple, and chemical-free method of producing nanoparticles. The present work reports the synthesis of Murraya koenigii-mediated ZrO2 nanoparticles (ZrO2 NPs) and their applications as a photocatalyst and antibacterial agent. Capping and stabilization of metal oxide nanoparticles were achieved by using Murraya koenigii leaf extract. The optical, structural, and morphological valance of the ZrO2 NPs were characterized using UV-DRS, FTIR, XRD, and FESEM with EDX, TEM, and XPS. An XRD analysis determined that ZrO2 NPs have a monoclinic structure and a crystallite size of 24 nm. TEM and FESEM morphological images confirm the spherical nature of ZrO2 NPs, and their distributions on surfaces show lower agglomerations. ZrO2 NPs showed high optical absorbance in the UV region and a wide bandgap indicating surface oxygen vacancies and charge carriers. The presence of Zr and O elements and their O=Zr=O bonds was categorized using EDX and FTIR spectroscopy. The plant molecules’ interface, bonding, binding energy, and their existence on the surface of ZrO2 NPs were established from XPS analysis. The photocatalytic degradation of methylene blue using ZrO2 NPs was examined under visible light irradiation. The 94% degradation of toxic MB dye was achieved within 20 min. The antibacterial inhibition of ZrO2 NPs was tested against S. aureus and E. coli pathogens. Applications of bio-synthesized ZrO2 NPs including organic substance removal, pathogenic inhibitor development, catalysis, optical, and biomedical development were explored.