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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. [ABSTRACT FROM AUTHOR]