Cu-Mn co-doped ZnSe quantum dots were eco-friendly synthesized at different synthesis conditions using water-based microwave-activated (MWIR) method. Energy band gaps EDASFgap were determined using high-precision derivation of absorption spectrum fitting (DASF) method; the obtained results show that EDASFgap values are within the range of 3.49–3.77 eV. Depending on the synthesis conditions, a decreasing trend of energy gap was observed with the increasing of MWIR time and ambient temperature. Morphologies and structural characterizations were done by XRD, EDX, FESEM, map and TEM, which revealed formation of ZnSe nanoparticles with mean crystallite size of ~ 2–5 nm. Also, Urbach energies were estimated, which their very small values in compare with Egap imply to the sharp band edges and so their good crystallinity nature. Moreover, refractive index, dielectric constant and nonlinear optical susceptibility of each sample were determined; results imply that these nanoparticles have a high potential in optoelectronic applications. Also, structural characteristics such as dislocation density, lattice strain and size of NCs were evaluated upon the Scherrer, Williamson–Hall and Williamson–Smallman methods. The results of structural features obtained from these approaches are highly inter-correlated and show same trends with the variation of synthesis conditions. Results show that the size of QDs is varied tunable by changing the MWIR time, ambient temperature and Mn dopant percentage and the as-synthesized ZnSe QDs and doped QDs have similar cubic zinc blend structure. Also, TEM result reveals that ZnSe nanoparticles are spherical in shape with an average grain size of about 5 nm. Upon the different performed opto-structural criteria, sample with Mn = 4% has the best crystallinity as good candidate in optical and mechanical applications. There were anomalies in different properties at Mn = 1.5 and 2% attributed to their higher density of lattice imperfections and surface t
