Even with significant developments in nanoscience, fairly little is known about the interactions of nanocrystal semiconducting materials with bio-macromolecules. These interactions can influence the properties of both nanocrystals and bio-macromolecules. Understanding this interface is a condition to apply both nanoparticles and biomolecules for bioengineering. To investigate the interfacial phenomena of cadmium selenide quantum dots (CdSe QDs) nanocrystals with proteins extracted from Moringa oleifera seeds, different concentrations of cadmium selenide quantum dots-Moringa oleifera seed protein (CdSe—MSP) complexes were prepared. Respective CdSe QDs with hexagonal phase and crystalline size in the range of 4—7 nm were synthesized and labelled with the purified mesoporous MSP having a surface area of 8.4 m2/g. The interaction mechanism between CdSe QDs and MSP was studied using the UV-Vis absorption spectroscopy, fluorescence emission spectroscopy and Fourier Transform Infrared spectroscopy. The UV-Vis absorption spectrum showed an absorption band of CdSe-MSP complexes at 546.5 nm. The lowest absorbance intensity was observed for the complex with the highest concentration of M. oleifera seed proteins. The fluorescence (FL) spectroscopy of the complex was excited at 280 nm wavelength and emission was monitored at 598 nm. FL intensity of CdSe QDs was found to decrease with an increasing concentration of MSP. Using Stern-Volmer analysis, the binding constants (Kb), quenching constants (Kq) and the number of binding sites (n) were determined. The thermodynamic potentials ∆Hθ(—321.3 kJmol—1);\ ∆Sθ( 156.0 JK—1mol—1) and ∆Gθ(—46.6 kJmol—1) were also calculated. The complexes could be classified as the dynamic quenching mechanism. In the previous studies, the standard quenchers, viz. acrylamide, iodide and nitrate were used to quench the fluorescence of the MSP whereas in this study the protein has acted as a quencher of QDs fluorescence. The stability of the complex is strongly influenced by the CdSe QDs adsorbed into MSP through electrostatics interaction and surface-bound complexation equilibrium attraction. This information can help to elucidate the surface characteristics of MSP and its potential interactions with other molecules or nanoparticles.