Glass-embedded Cd1−xCoxS quantum dots (QDs) with mean radius of R ≈ 1.70 nm were successfully synthesized by a novel protocol on the basis of the melting-nucleation synthesis route and herein investigated by several experimental techniques. Incorporation of Co2+ ions into the QD lattice was evidenced by X-ray diffraction and magnetic force microscopy results. Optical absorption features with irregular spacing in the ligand field region confirmed that the majority of the incorporated Co2+ ions are under influence of a low-symmetry crystal field located near to the Cd1−xCoxS QD surface. Electron paramagnetic resonance data confirmed the presence of Co2+ ions in a highly inhomogeneous crystal field environment identified at the interface between the hosting glass matrix (amorphous) and the crystalline QD. The acoustic-optical phonon coupling in the Cd1−xCoxS QDs (x ≠ 0.000) was directly observed by Raman measurements, which have shown a high-frequency shoulder of the longitudinal optical phonon peak. This effect is tuned by the size-dependent sp-d exchange interaction due to the magnetic doping, causing variations in the coupling between electrons and longitudinal optical phonon. Copyright © 2013 John Wiley & Sons, Ltd.