Treatment of dry M2+-exchanged zeolite Y (M2+ = Cd2+, Mn2+, and Zn2+) with dry H2S leads to the formation of isolated, ligand-free, subnanometer MS quantum dots (QDs) in zeolite Y with no framework destruction and with H+ as the countercation. Treatment of the dry H+/CdS QD-incorporating zeolites Y with dry NH3 leads to the neutralization of H+ to NH4+. During this process, the framework structure remains intact. However, small amounts of interconnected CdS QDs were formed within the zeolite Y by coalition of isolated CdS QDs at the windows. With H+ as the countercation, isolated CdS QDs rapidly aggregate into interconnected and mesosized QDs with accompanying destruction of similar to 50% of sodalite cages leading to the framework rupture. With NH4+ as the countercation, however, the isolated QDs and zeolite framework remain intact even after exposure to the moist air for 4 weeks. Interestingly, the interconnected QDs that were formed during neutralization of H+ with NH3 disintegrate into isolated QDs in the air. Similar results were obtained from ZnS and MnS QDs generated in zeolite Y. Thus, ligand-free, naked, subnanometer QDs can now be safely preserved within zeolite pores under the ambient conditions for long periods of time. This finding will expedite the generation and dispersion of various QDs in zeolite pores, their physicochemical studies, and applications.