An aqueous-based green route has been demonstrated for the preparation of ZnSe quantum dots (QDs) and doping of transition metals in the presence of thiol mercaptopropionic acid (MPA) as growth moderator by refluxing at 100 °C. The structure and morphology of synthesized ZnSe quantum dots have been investigated by using X-ray diffraction studies (XRD), Ultraviolet–Visible spectroscopy (UV–vis), Fourier Transform Infrared Spectroscopy (FTIR) and Photoluminescence (PL) Spectroscopy. XRD studies indicate the structure of the quantum dots is cubic with diameters in the range of 4–5 nm. Fourier Transform Infrared (FTIR) studies proves that MPA ligands were bound strongly on the ZnSe nanocrystal surface as thiolate. The band gap energy (Eg) was calculated to be 3.8 eV which is blue shifted from the standard value of bulk band gap (2.60–2.70eV. Photoluminescence spectra shows broad emission value ranging between 400 and 700 nm due to surface defects which has been reduced by doping with transition metals (Fe, Co, Ni, Cd) in aqueous medium. The effective passivation of trap luminescence is done by doping leading to increase in photoluminescence quantum yield specifically with nickel and cadmium doped ZnSe QDs.