Control of Infectious diseases such as; bacteria and viruses, has become a globally critical issue, since the appearance of COVID-19 virus in 2020. In addition to the microbial resistance of the currently available therapeutic drugs as well as, its prolonged side effects make its use is of health care concern. Green nanotechnology approach is a promising solution for controlling such infectious diseases and many biomedical purposes. In the present study, green synthesis approach based on microwave-assisted hydrothermal method is an innovative and environmentally friendly method for preparation of bioactive CeO2 and ZnO nanorod structured materials using Olea europaea (O. e.) leaf plant extract as a natural medicinal capping agent for controlling the shape and size of nano-products. The optical and structural analyses of the obtained nanorod-structures are characterized using; TEM, FTIR, XRD, SBET analyses and particle size analyzer. The green-synthesized ZnO and CeO2 nanorods display an average crystallite size of approximately 15 and 5 nm, respectively. The antimicrobial activity of ZnO and CeO2 nanorods compared with the traditional hydrothermal methods, was examined on six clinical pathogens including; (E. coli Serratia sp., S. aureus, Bacillus subtilis, Streptococcus mutant, and MRSA). The results indicated superior antimicrobial and anti-tumor activities towards hepatocellular carcinoma cell lines (IC50 = 117.24 and 103.50 μg mL−1 for ZnO and CeO2 and LD50 > 3000 mg kg−1). This demonstrates that the green microwave process is a promising approach for the synthesis of effective ZnO and CeO2 nanomaterials applied for many biomedical applications.