© 2022, The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.CuFe2O4, ZnFe2O4, and MnFe2O4 ferrite nanoparticles (NPs) have been synthesized through auto composition sol–gel method, and citric acid was used as the chelating agent. Phase analysis of nanoparticles confirmed the pure cubic spinel structure. The morphology and elemental composition verified the presence of all the elements in prepared samples and size distribution of NPs was estimated to be ~ 20–30 nm. Saturation magnetizations and magneton numbers were in the range of 53–67 emu/g and 2.29–3.12 nB, respectively. MnFe2O4 NPs exhibited the strongest magnetization of all NPs. Highly significant antibacterial activity (22 mm zone of inhibition) of CuFe2O4 NPs was observed against Gram negative bacteria, Escherichia coli. The broth microdilution assay result demonstrated the lower minimum inhibitory concentration and minimum bactericidal concentration values for CuFe2O4 as well as for ZnFe2O4 and MnFe2O4 NPs in combination. Furthermore, the in vitro cytotoxicity assay revealed that NPs were not toxic to HSF 1184 cell lines at 400 μg/ml concentration, hence the prepared NPs are safe, affordable, sustainable composite and can be used for potent antibacterial applications. Graphical Abstract: [Figure not available: see fulltext.].