In this paper, an aqueous-based approach is introduced for facile, fast, and green synthesis of gradient-alloyed Fe-doped ZnSe(S)@ZnSe(S) core:shell quantum dots (QDs) with intense and stable emission. Co-utilization of co-nucleation and growth doping strategies, along with systematic optimization of emission intensity, provide a well-controllable/general method to achieve internally doped QDs (d-dots) with intense emission. Results indicate that the alloyed ZnSe(S)@ZnSe(S) core:shell QDs have a gradient structure that consists of a Se-rich core and a S-rich shell. This gradient structure cannot only passivate the core d-dots by means of the wider band gap S-rich shell, but also minimizes the lattice mismatch between alloyed core–shell structures. Using this novel strategy and utilizing the wider band gap S-rich shell can obviously increase the cyan emission intensity and also drastically improve the emission stability against chemical and optical corrosion. Furthermore, the cytotoxicity experiments indicate that the obtained d-dots are nontoxic nanomaterials, and thus they can be considered as a promising alternative to conventional Cd-based QDs for fluorescent probes in biological fields. Finally, it is demonstrated that the present low-toxicity and gradient-alloyed core:shell d-dots can be used as sensitive chemical detectors for Pb2+ ions with excellent selectivity, small detection limit, and rapid response time.