Luminescent semiconductor quantum dots (QDs) are frequently used in the life and material sciences as reporter for bioimaging studies and as active components in devices such as displays, light-emitting diodes, solar cells, and sensors. Increasing concerns regarding the use of toxic elements like cadmium and lead, and hazardous organic solvents during QD synthesis have meanwhile triggered the search for heavy-metal free QDs using green chemistry syntheses methods. Interesting candidates are ternary AgInS2 (AIS) QDs that exhibit broad photoluminescence (PL) bands, large effective Stokes shifts, high PL quantum yields (PL QYs), and long PL lifetimes, which are particularly beneficial for applications such as bioimaging, white light-emitting diodes, and solar concentrators. In addition, these nanomaterials can be prepared in high quality with a microwave-assisted (MW) synthesis in aqueous solution. The homogeneous heat diffusion and instant temperature rise of the MW synthesis enables a better control of QD nucleation and growth and thus increases the batch-to-batch reproducibility. In this study, we systematically explored the MW synthesis of AIS/ZnS QDs by varying parameters such as the order of reagent addition, precursor concentration, and type of stabilizing thiol ligand, and assessed their influence on the optical properties of the resulting AIS/ZnS QDs. Under optimized synthesis conditions, water-soluble AIS/ZnS QDs with a PL QY of 65% and excellent colloidal and long-term stability could be reproducible prepared.