Quantum dots (QDs) synthesized from environmentally friendly precursors associated to scalable and high-efficiency production routes are essential for nanomedicine applications. Ag2S nanocrystal is notable by antimicrobial activity, photothermal properties, and low toxicity, making it promising bioactive nanomaterial. In this work, L-glutathione (GSH) capped Ag2S and ZnSe seeds were synthesized by using a fast and environmentally friendly electrochemical method (cavity cell, graphite powder macroelectrode and aqueous medium) and tested for biological applications. Ag2S nanocrystals presented a monoclinic structure (XRD analysis). The modulation of the optical properties was carried out by varying the Ag+/S2- ratio (1:1, 2:1, and 4:1), showing a photoluminescence hypsochromic shift from 916 to 759 nm, respectively. The modulation of the optical parameters was also carried out by the synthesis of Ag2S@ZnSe core/shell nanostructures. ZnSe seeds were prepared by the same electrochemical method and added to the Ag2S solution followed by thermal treatment under reflux (10 min). Ag2S@ZnSe systems showed higher photoluminescence intensity and a hypsochromic shift of the emission band using Ag2S cores (Ag+/S2- = 1:1 and 1:2), which was associated to the formation of alloy-type structures. In the case of the Ag2S@ZnSe (Ag+/S2- = 1:4), a bathochromic shift of the emission bands can be observed, which was associated to the formation of a core/shell structure. Ag2S@ZnSe QDs were tested in antimicrobial and cytotoxicity assays, showing a minimal inhibitory concentration (MIC) equal to 512 µg.mL−1. No cytotoxicity was observed against the Vero cell line at all concentrations tested (7.81–1000 µg.mL−1), and low cytotoxicity against the HT-29 tumor line (7.81–31.25 µg.mL−1), thus showing promising results for bioapplications.