Copyright © 2020 American Chemical Society. Multinary semiconductor quantum dots (QDs) that have less toxicity and show near-infrared light responsivity have attracted much attention for in vivo bioimaging. In this study, we controlled the optical properties of Ag-In-Se QDs by modulating the nonstoichiometry and the degree of Ga3+ doping. Precise tuning of the Ag/In ratio of Ag-In-Se QDs enabled a sharp band-edge emission to emerge without broad defect-site emission. Ga3+ doping into Ag-In-Se (AIGSe) QDs enlarged their energy gap, resulting in a blue shift of the band-edge PL peak from from 890 to 630 nm. The band-edge PL intensity was remarkably enlarged by surface coating with a thin GaSx shell followed by treatment with trioctylphosphine, the highest PL yield being 38% for the PL peak at 800 nm. Thus-obtained QDs were successfully used as near-IR PL probes for three-dimensional in vivo bioimaging in which the wavelengths of excitation and detection lights could be selected in the first biological window, and then the signals were clearly detected from AIGSe@GaSx core-shell QDs injected into biological tissues by ca. 5 mm in depth.