This article examines the physicochemical conditions governing the formation of the Qarah-bagh phlogopite deposit, considering the characteristics of its mineral assemblage and tectono-magmatic context. This Late Paleozoic deposit is located on the alkali-granite margin and in contact with older metamorphic rocks. In fact, the deposit is related to bimodal magmatism associated with the Neo-Tethys rift. The mineral assemblage of the deposit includes phlogopite + calcite + apatite ± chlorite ± epidote ± pyroxene ± pyrite. Phlogopite shows Mg#>0.88 and Mg-rich exsolution lamellae. The pyroxene composition is characterized as Wo0.53En0.45Fs0.02 and exhibits an irregular and disequilibrium rim with fine-grained minerals such as chlorite and epidote. The minerals of chlorite, epidote, and apatite are of the Mg-, Fe3+-, and F-bearing type, respectively. Apatite appears as coarse prisms, homogeneous, without chemical zoning, and with abundant microcracks and microporosity. The significant occurrence of silicate, carbonate, and phosphate minerals in this assemblage may be evidence of the involvement of immiscible liquids in its genesis. The apatite and pyroxene of the assemblage were the first phases to crystallize. Calcite and phlogopite are from the final phases of crystallization and probably originated from a carbonate melt or its interaction with a silicate melt in the final stages. Other minerals in this assemblage, such as chlorite, epidote, and pyrite, were formed by propylitic alteration.