This study investigates the impact of zirconium substitution on the structural, elastic and magnetic properties of CoCr2O4 nanoparticles. A series of CoCr2−xZrxO4 nanoparticles, x = 0.00, 0.05, 0.10, 0.15 and 0.20, are synthesized via the co-precipitation method. X-ray diffraction (XRD) patterns affirm the formation of single-phase cubic structure with the space group Fd3m. Special attention is given to accurately calculating the average crystallite size (D) and lattice parameter (a) using Williamson–Hall (W–H) analysis and the Nelson–Riley (N–R) extrapolation function, respectively. The increase in Zr4+ content leads to a reduction in crystallite size and an increase in the lattice parameter. Elastic properties are estimated from force constants and the lattice constant, determined from FTIR and XRD, respectively. The observed changes in the elastic constants are attributed to the strength of interatomic bonding. The stiffness constants decrease, while Poisson’s ratio increases with increasing Zr4+ content, reflecting the increase in the ductility of the prepared samples. As the Zr4+ content increases, the stiffness constants decrease, and Poisson’s ratio increases, reflecting enhanced ductility of the samples. Furthermore, as Zr4+ content rises, Young’s modulus, the rigidity modulus and Debye temperature decrease. The magnetic hysteresis loop measurements are carried out at room temperature using a vibrating sample magnetometer (VSM) over a field range of 25 kg. Unsubstituted CoCr2O4 exhibits ferrimagnetic behavior. As Zr4+ content increases, saturation magnetization (Ms) and magnetic moment decrease, while remanent magnetization (Mr) and coercivity (Hc) initially decrease up to x = 0.10, then increase with further increases in x. The novel key of this study is how Zr4+ substitution in CoCr2O4 nanoparticles can effectively modify their elastic moduli and magnetic properties, making them suitable for various applications such as flexible electronics, protective coatings, energy storage components and biomedical implants.