We investigate the effect of Co2+ ion doping in magnetite (Fe3O4) on its crystal structure, magnetic properties, and phase stability during air and vacuum annealing. The nanoparticles are prepared by co-precipitation method and the particles are characterized by XRD, small angle x-ray scattering (SAXS), themogravimetric and differential scanning calorimetry (DSC), and vibrating sample magnetometer. The SAXS analysis on the doped samples show the most probable size, shape, and the polydispersity of particles, synthesized with different fractions (0–0.6) of Co2+ ion doping remains almost the same. On increasing cobalt content ferrimagnetic to the antiferromagnetic hematite (α-Fe2O3) phase transformation temperature is found to increase dramatically. For 0.1 fraction of Co2+ metal ion doping, an enhancement of 100 °C in the γ-Fe2O3 to α-Fe2O3 phase transition temperature is observed in the air annealed samples, whereas magnetic nature remains stable up to 1000 °C in vacuum annealed samples. On increasing the cobalt fractions beyond 0.2, air annealed samples show no change in the phase transition temperature. The observed enhancement in the phase transition temperature is attributed to the increased activation energy for phase transformation in presence of Co2+. Further, the DSC results corroborate the finding of an increase in the maghemite to hematite phase transition temperature with increase in cobalt fraction (x). The decrease in enthalpy from 89.86 to 17.62 J g-1 with an increase in cobalt content indicates that the degree of conversion of maghemite to hematite decreases with the cobalt content, which is in good agreement with the Rietveld analysis. The decrease in the Ms value in air annealed sample is attributed to the re-distribution of cations - n the tetrahedral and octahedral sites, as the Fe3+A-Fe3+B super-exchange interaction is different from the Co2+A-Fe3+B interaction. These results suggest that a very small percentage of Co2+ metal ion doping can dramatically enhance the thermal stability of magnetic nanoparticles, which will have important consequences on the phase stability of ferrite nanocrystals.