In recent years, the marked augment of antibiotic resistance hampered the development of antibacterial agent. Nanozymes by their in situ ROS production capability oxidize cellular substances of bacterial cell and eliminate MDR bacteria. Therefore, synthesis of effective nanozymes from green precursors is rarely reported, so the prime objective of this study was to synthesize Cu-MnO nanozymes from aqueous extracts of medicinal plant Azadirachta indica via co-precipitation approach and to endorse their biomedical applications. The synthesized materials were characterized by X-ray diffraction (XRD), Fourier Transform Infrared spectrometer (FTIR), Scanning Electron Images (SEM), and Field-Emission Scanning Electron Microscopy (FESEM) images. X-ray Diffraction (XRD) patterns revealed the formation of hausmannite MnO crystal system. Fourier Transform Infrared spectrometer (FTIR) spectra revealed functional groups on the surface nanoparticles for their stabilization. Energy-Dispersive X-ray spectroscopy (EDAX) profile confirmed the existence of desired elements in the synthesized nanozymes. B1 mimics oxidase enzyme most effectively with K = 0.175 mM and V = 10.34 µM/min. The low K and high V indicates the strong binding affinity and high catalytic activity. From the agar diffusion antibacterial assay, it can be concluded that B3 is the most potent antibacterial agent specifically against Gram-positive bacteria Bacillus subtilis with inhibition zone of 27 mm at 250 µg/mL. Their cytotoxic activities on neuroblastoma (SHSY5) cell line were investigated for the first time. The data revealed that synthesized nanooctahedrons possess a significant cytotoxicity against cancer cell lines SHSY5Y (IC = 137.47 ± 14.11 µg/mL) and SKOV3 (IC = 72.72 ± 9.33 µg/mL). Overall, with increasing Cu amount, the percentage growth inhibition of MnO crystal system enhanced. The improved antibacterial activity and cytotoxicity is due to synergy between metal and phytochemicals. Radical scavenging activity of synthesized nanozymes is comparatively lower than their green source and the comparatively lower IC values of B1, 234.12 ± 15.13 and 220.12 ± 10.37 respectively, which indicates that it is more active in scavenging DPPH and ABTS radical. B2 (IC = 310.56 ± 5.92 µg/mL) and B3 (IC = 43.56 ± 3.03 µg/mL) scavenge superoxide radicals and FRAP more effectively. It is noticed that synthesized nanozymes have greater antibacterial and anticancer activity but low scavenging ability compared to green extract. Thus, Cu-MnO NPs from Azadirachta indica leaf extract could be utilized as a replacement of potential antibiotic drug candidate against MDR bacteria and in cancer avenues.