In this work, manganese (Mn)-doped CuInSe quantum dots (QDs) with a ZnS passivation layer (MnCuInSe/ZnS) have been synthesized via a one-pot microwave-assisted hydrothermal reaction using glutathione (GSH) as a stabilizer. The MnCuInSe/ZnS core-shell QDs combine magnetic resonance imaging (MRI), excitation-dependent red emission, and reactive oxygen radical generation functions, in which regulation of Mn2+ incorporation leads to synergistic imaging and therapeutic modalities. The MnCuInSe/ZnS QDs exhibit high colloidal and photochemical stability in simulated media and at different pH values. An r2/r1 ratio of 9.99 was calculated from MRI studies suggesting their potential application as dual-modal imaging agents. Based on in vitro tests on Hela, B16, and HepG2 cell lines, it is apparent that MnCuInSe/ZnS QDs impose no significant cytotoxicity in the dark, while they can efficiently generate singlet oxygen radicals for photodynamic therapy of cancers, killing more than 80% of B16 cells within 5 min of laser irradiation (671 nm, 1 W cm−2). Furthermore, in vitro fluorescence imaging and cellular internalization of QDs are examined to visualize cellular uptake and in situ ROS generation. Therefore, this research exemplifies a new set of multifunctional chalcogenide QDs for theranostic applications.