The Mn0.92Cu0.08‐yZnyFe2O4 (y=0.02, 0.04, 0.06 and 0.08) nanoparticles (MCZF NPs) were synthesized via the hydrothermal process at low operating temperature. The MCZF system generated a cubic spinel structure as seen by the X‐ray diffraction patterns. The average crystallite size was observed to be increasing from 25 to 30 nm. The broad (γ1) and narrow (γ2) absorption bands were seen in FTIR spectra and the cation distributions at tetrahedral (A) and octahedral (B) sites, respectively, was indicated. The surface morphology was analyzed using electron microscopy. Clarification was provided for the dependence of the optical bandgap shift (Eg~1.96–2.15 eV) on the concentration of substituent. The superparamagnetic nature of MCZF can be advantageous for biomedical applications and it was demonstrated by the magnetization versus applied magnetic field (M−H) loops. Small values of remanence magnetization (Mr) and coercivity (Hc) were found using magnetization versus magnetic field (M−H) curves at y=0.02, 0.04, 0.06, and 0.08. This proved that MCZF NPs exhibited the superparamagnetic behavior. The cation distribution at two sublattices was also estimated using a two‐sublattice model. The greatest zone of inhibition in an antibacterial study of MCZF (produced by the green method) was 10.8 mm for Pseudomonosa aeruginosa and 9.4 mm for Staphylococcus aureus.