ZnSe:Cu d-dots and ZnSe:Cu@ZnS core/shell quantum dots (QDs) were synthesized under different synthesis regimes of Cu-dopant content, microwave irradiation time (MWIRT) and over-coating of ZnSe:Cu by ZnS shell in order to optimize their structural and photoluminescence (PL) properties. The morphological and microstructural characterizations broadly done by transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDS) and X-ray diffraction (XRD), revealed the spherical shape, synthesis-condition tunable and almost uniform size distribution of bare and core/shell QDs. Extended X-ray diffraction analysis (XDA) was performed by employing both Williamson-Hall (W–H) and Williamson-Smallman (W–S) approaches in order to validate these methods and obtain lattice strain (ε), dislocation density (δ) and particle size. The results indicated that all the QDs had cubic zinc-blend structure with an average crystallite size of ~1.5 nm, and shift of peak positions shift toward higher angles for core/shells compared with bare QDs. W–S and W–H’s outputs for bare and core/shell QDs showed similar trends, i.e. the optimal Cu-content of 0.1 mol% with higher crystalline quality. In addition, bare and core/shell QDs were investigated by Ultraviolet–Visible and PL spectroscopy. The blue-shift of band gap for the synthesized ZnSe QDs (~3.5 eV) in comparison with bulk counterpart (~2.7 eV) confirmed the formation of nano-sized particles. It was found that these QDs exhibited PL emission in the range of 423–559 nm. After changing the experimental variables during the experiment, the samples with optimal PL were identified. In reasonable relation to the microstructural aspects, ZnSe:Cu(1.5%) under MWIRT = 6 min has the highest band-edge PL intensity, which was associated with increased particle size, reduced lattice strain and higher atomic order raised from MWIR. Among the core/shell QDs, ZnSe:Cu(1.5%)@ZnS under MWIR ind