A facile synthesis method is introduced how to prepare magnetically active ultraviolet emitting manganese ions incorporated into ZnS x Se1−x colloidal quantum dot (nanoalloy) at 110 °C in aqueous solutions. The reaction time is the main factor to control the hydrodynamic size from 3 to 10 nm and the precursor ratio is significant to tune the alloy composition. ZnS shell layer on the ZnS x Se1−x core was grown to passivate environmental effects. The nanoalloy has ultraviolet emission at 380 nm having a lifetime of 80 ns and 7% quantum yield. The incorporation of Mn2+ ions into the nanoalloys induced magnetic activity but did not modify the structure and photophysical properties of the nanoalloys. Colloidal and powdery samples were prepared and analyzed by electron paramagnetic resonance (EPR) spectroscopy. In the colloidal dispersions, EPR spectra showed hyperfine line splitting regardless of the Mn2+ ion fractions, up to 6%, indicating that Mn2+ ions incorporated into the nanoalloys were isolated. EPR signals of the powdery samples were broadened when the fraction of Mn2+ ions was higher than 0.1%. The EPR spectra were simulated to reveal the locations and interactions of Mn2+ ions. The simulations suggest that the Mn2+ ions are located on the nanoalloy surfaces. These findings infer that the magnetic dipolar interactions are regulated by the initial mole ratio of Mn/Zn and the physical state of the nanoalloys adjusted by preparation methods.