The present research work focuses on preparing 3D transition metal doped copper oxide nanostructures through sonication method and to investigate the effect of doping different transition metal into copper oxide (CuO) on the basic properties of CuO nanoparticles and, to study the photocatalytic behaviour of the doped CuO samples. The morphological studies performed with the help of SEM revealed the formation of flower like CuO 3D nanostructures for all the doped samples. The slight shift in the position of peaks in the x-ray diffraction (XRD) pattern confirms that doping has been successfully done into CuO. Also, the sharp diffraction peaks suggest the polycrystalline nature of the sample with monoclinic structure. The UV–vis absorption analysis reveals a bandgap of 2.26, 2.12 and 2.15 eV for the CuO samples doped with nickel, zinc, and iron respectively via Tauc plot. The photocatalytic performance of the samples tested through the degradation of methylene blue (MB) dye suggests that samples doped with Zn shows better degradation. Thus, it is evident that the morphology and the optical properties of the CuO can be tailored by doping transition metal into it. •Flower-like 3D CuO nanostructures doped with transition metals (Ni, Fe and Zn).•As the atomic radius of Cu, Ni, Zn and Fe are 0.73 Å, 0.69 Å, 0.70 Å and 0.74 Å.•Fe doped samples reveal a bandgap of 2.12 eV and 2.15 eV respectively.•Efficiency of photo-degradation of the Ni −52 %, Zn-63 %, and Fe-62 % doped samples.•After exposing the test solution for 60 min a very good degradation result.