We experimentally report the control of structural inhomogeneity and magnetic properties of Co-doped ZnO films using nitrogen mediated-crystallization. The ZnO:CoN were grown on a silicon substrate at room temperature by RF-magnetron sputtering using nitrogen and followed by a post-annealing treatment for 3 hours at 400 °C, 600 °C, 800 °C and 1000 °C in the air. This method induces changes in inhomogeneity properties comprised by microstructure and stoichiometry of each film, which are confirmed by X-ray diffraction, thermal desorption, and X-ray fluorescence measurements. The difference in inhomogeneity has led to the transformation in the magnetic properties. Films annealed at 400 °C, which showed the highest inhomogeneity, exhibited superparamagnetic-ferromagnetic properties. In contrast, all the other films exhibited diamagnetic properties. Increasing the post-annealing temperature above 400 °C reduces inhomogeneities indicated by improved grain size, decreased impurities, and lattice parameters and stoichiometry of ZnO:CoN films approached those of pure ZnO. Our present results will contribute to control the inhomogeneity of ZnO:Co films to improve magnetic properties at room temperature.