Low-dimensional III-V semiconductors have many advantages over other semiconductors; however, they are not particularly stable under physiological conditions. Hybridizing biocompatible organic molecules with advanced optical and electronic semiconductor devices based on quantum dots (QDs) and quantum wires could provide an efficient solution to realize stress-free and nontoxic interfaces to attach larger functional biomolecules. Monitoring the modifications of the optical properties of the hybrid molecule-QD systems by grafting various types of air-stable diazonium salts onto the QD structures surfaces provides a direct approach to prove the above concepts. The InAs/GaAs QD structures used in this work consist of a layer of surface InAs QDs and a layer of buried InAs QDs embedded in a wider-bandgap GaAs matrix. An enhancement in photoluminescence intensity by a factor of 3.3 from the buried QDs is achieved owing to the efficient elimination of the dangling bonds on the surface of the structures and to the decrease in non-radiative recombination caused by their surface states. Furthermore, a narrow photoluminescence band peaking at 1620 nm with a linewidth of 49 meV corresponding to the eigenstates interband transition of the surface InAs QDs is for the first time clearly observed at room temperature, which is something that has rarely been achieved without the use of such engineered surfaces. The experimental results demonstrate that the hybrid molecule-QD systems possess a high stability, and both the surface and buried QDs are very sensitive to changes in their surficial conditions, indicating that they are excellent candidates as basic sensing elements for novel biosensor applications.