Ligand-induced chirality in semiconducting nanocrystals has been the subject of extensive study in the past few years and shows potential applications in optics and biology. Yet, the origin of the chiroptical effect in semiconductor nanoparticles is still not fully understood. Here, we examine the effect of the interaction with amino acids on both the fluorescence and the optical activity of chiral semiconductor quantum dots (QDs). A significant fluorescence enhancement is observed for L/D-Cys-CdTe QDs upon interaction with all the tested amino acids, indicating suppression of non-radiative pathways as well as the passivation of surface trap sites brought via the interaction of the amino group with the CdTe QDs’ surface. Hetero-chiral amino acids are shown to weaken the Circular Dichroism (CD) signal, which may be attributed to a different binding configuration of cysteine molecules on the QDs surface. Furthermore, a red shift of both CD and fluorescence signals in L/D-Cys-CdTe QDs is only observed upon adding cysteine, while other tested amino acids do not exhibit such an effect. We speculate that the thiol group induces orbital hybridization of the highest occupied molecular orbital (HOMOs) of cysteine and the valance band of CdTe QDs, leading to the decrease of the energy band-gap and a concomitant red shift of CD and fluorescence spectra. This is further verified by density functional theory (DFT) calculations. Both the experimental and theoretical findings indicate that the addition of ligands which do not “directly” interact with the VB of the QD (non-cysteine moieties) changes the QD photophysical properties as it probably modifies the way cysteine is bound to the surface. Hence, we conclude that it is not only the chemistry of the amino acid ligand which affects both CD and PL, rather, it is also the exact geometry of binding which modifies these properties. Understanding the relationship between QD’s surface and chiral amino acid thus provides an additional perspective on the fundamental origin of induced chiroptical effects in semiconductor nanoparticles, potentially enabling us to optimize the design of chiral semiconductor QDs for chiroptic applications.