Zn-substituted cobalt ferrite-based ferrofluids (FFs) were successfully synthesized using a modified co-precipitation method. In this study, we aimed to investigate the heating performance of the synthesized FFs using a resonance coil-based magnetic hyperthermia setup and characterize their viscoelastic behaviour using a magneto rheometer. The crystalline spinel phase with Fd3m (227) symmetry was confirmed through Powder X-ray Diffraction (PXRD. Additionally, Vibrating Sample Magnetometer (VSM) measurements allowed us to analyze the effect of Zn substitution on the room temperature magnetic properties of the FFs. To gain insights into the viscoelastic properties, steady-state rheological measurements were performed. The FFs exhibited non-Newtonian behaviour at low shear rates (<100 s−1) and transitioned to Newtonian fluid behaviour at higher shear rates. Furthermore, we investigated the magneto-viscoelastic behaviour of the FFs across a range of magnetic field strengths (0 to 1 T) using three different fluids. It was observed that the viscosity increased as the field strength increased, which can be attributed to the formation of chain-like structures. The heating efficiency of the FFs was evaluated in terms of Specific Absorption Rate (SAR) using the Initial Slope Method (ISM) and Box Lucas Method (BLM). The SAR values for the FFs exhibited a significant increase with Zn substitution, with the maximum values recorded as 188 ± 8 W/g (ISM) and 212 ± 9 W/g (BLM) for Zn0.4Co0.6Fe2O4, surpassing the SAR value of CoFe2O4 (72 ± 8 W/g, ISM; 92 ± 5 W/g, BLM). To assess biocompatibility, we conducted a cell viability assay using HEK-293 cell lines. The results demonstrated high cell viability (>75%) for Zn0.4Co0.6Fe2O4 at a concentration of 100 µg/ml after a 48-hour incubation period.