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The synthesis of iron oxide nanoparticles (IONPs)–antiubiquitin antibodies (Abs) complex for depletion of dead/damaged spermatozoa from buffalo semen was done. The IONPs synthesized were round in shape with size of 12.09 ± 0.91 nm. At the end of the two‐step functionalization, that is, silanization and pegylation of bare IONPs and bioconjugation of functionalized IOPNs, particles with the sizes of 19.15 ± 1.46, 20.72 ± 0.95, and 73.01 ± 7.56 nm, respectively, were obtained. Twenty‐four semen samples from four bulls with mean individual progressive motility (%) and sperm concentration (million/mL) of 77.1 ± 0.9 and 1,321.2 ± 84.7, respectively, were divided into Group I (control), and treatment groups viz. Groups II, III, and IV; with each group containing 150 ± 25 million dead/damaged spermatozoa. The IONPs–Abs complex was added at the ratio of 1:1 (0.5 μg/mL), 1:2 (1.0 μg/mL), and 1:4 (2.0 μg/mL), respectively, in the Groups II, III, and IV. The mean efficiency (%) of nanopurification was estimated to be greater in nanopurified semen with the increasing doses of the IONPs–Abs complex. A reduction of 29.3 ± 6.4%, 48.4 ± 5.3%, and 55.4 ± 4.4% in dead/damaged spermatozoa following nanopurification in Groups II, III, and IV, respectively, was observed. The study shows that in‐house synthesized IONPs–Abs complex can be successfully used to deplete dead/damaged spermatozoa from buffalo semen with improvement in quality. [ABSTRACT FROM AUTHOR]