In the present study, spinel structure CoFe2O4 nanoparticles were successfully synthesized by the sol‐gel auto‐combustion technique. The effect of apple cider vinegar (ACV) addition as an organic biocompatible agent on the size, morphology, and magnetic properties of CoFe2O4 nanoparticles was investigated in detail. The phase evolution, particle size, and lattice parameter changes of the synthesized phase have been estimated by using Rietveld structure refinement analysis of X‐ray powder diffraction data. Also, Fourier transform infrared spectra (FT‐IR) of the samples verified the presence of two expected bands correspond to tetrahedral and octahedral metal‐oxygen complexes within the spinel structure. Furthermore, microstructural observations revealed that ultrafine particles have a semi‐spherical morphology. It was shown that the particles size decreased from ~45 to ~17 nm with an increase in the amount of ACV. Magnetic properties were carried out by vibrating sample magnetometer (VSM) at room temperature. Both the saturation magnetization (Ms) and coercivity (Hc) were found to be significantly dependent on the crystallite size and the amount of ACV.