Chalcopyrite quantum dots (QDs) have emerged as a safe alternative to cadmium-based QDs for bio-applications. However, the research on AgInS2 chalcopyrite QDs has not been widely explored in terms of their toxicity. Herein, we report a synthesis of biocompatible AgInS2/ZnS QDs via a greener approach. The emission intensity of the as-synthesized AgInS2 core QDs was enhanced 2-fold after the ZnS shell growth. X-ray diffraction revealed the tetragonal crystal structure of QDs, and high-resolution transmission electron microscope images show that the QDs are spherical in shape and crystalline in nature. Cell viability assays conducted on different cell lines, such as HeLa, A549, and BHK-21 cells, indicated that AgInS2/ZnS QDs are least toxic at a QD concentration range of 100 µg/mL. The fluorescent microscope analysis of A549 cells incubated with AgInS2/ZnS QDs shows that the QDs were accumulated in the cell membranes. The as-synthesized AgInS2/ZnS QDs are less toxic and eco-friendly, and can be used for biolabeling.