The formation of metastable strontium-yttrium(III) (hexakis) germanium(IV) lacunar apatite (P63/m, a=11.426Å, c=8.224Å and Z=2) was observed during the thermal treatment of SrCO3, Y2O3, and GeO2 powder precursors using the ceramic method in an oxygen atmosphere. The utilization of an oxygen atmosphere restricts the extensive reduction of GeO2 and enables us to explain a new potential mechanism for the stabilization of lead-free lacunar apatites. This mechanism involves the use of electrons localized in a neighborhood of oxygen vacancies. Charged vacancies serve as active sites for the ionosorption of oxygen molecules and their subsequent transformation into lattice oxygen anions, which fill the vacancies at the X-site. The estimation of system thermodynamics shows that apatite undergoes a transformation to a more stable state at δ≥0.1, i.e., at the value that corresponds to the composition of prepared apatite. As the temperature and time of the thermal treatment increases, the process of incongruent melting leads to the formation of oxygen-rich yttrium-germanium apatite (YGAp, Y9.333+ε[GeO4]6O2+3/2ε) and strontium-yttrium-germanium glass. The YGAp phase is also formed during the annealing of lacunar apatite in an oxygen atmosphere.