Abstract The present study concerns correlation of microstructure and magnetic properties of nanocrystalline binary 50Cu–50Co and ternary 50Cu–25Co–25Ni (wt%) alloys prepared by ball milling and subsequent isothermal annealing of the ball milled alloys. High resolution transmission electron microscopic (HR-TEM) investigation has shown deformation-induced microstructural features. Field emission scanning electron microscopy (FE-SEM) has revealed a distinct change in morphology of as-milled CuCoNi alloys after annealing. Differential scanning calorimetric (DSC) and X-ray diffraction (XRD) analysis have revealed that annealing of the CuCoNi alloy above 350 °C results into precipitation of nanocrystalline Co (fcc) in the CuNi matrix by spinodal decomposition. It is also demonstrated that isothermal annealing of the ball milled alloys in the temperature range between 350 and 650 °C significantly influence the magnetic properties, e.g. coercivity (Hc), remanence (Mr) and magnetic saturation (Ms) due to annihilation of defects such as stacking and twin fault along with dissolution and/or precipitation of magnetic phases in the Cu-rich matrix.