The results of mineralogical and thermobarogeochemical studies of lower-crustal xenolith of scapolite-bearing granulites from the fergusite-porphyry diatremes pipes in Southeastern Pamir (Tajikistan) are presented. All minerals (including garnet, clinopyroxene, and scapolite) of these granulites contain primary melt inclusions, which were studied using thermometric and microprobe methods (EPMA, SIMS, Raman spectroscopy). We have established that their compositions correspond to acid (from rhyodacites to rhyolites), essentially potassic melts of normal and high alkalinity with H2O ≤ 4 wt.%, Cl ≤ 0.8 wt.%, and CO2 ~ 1 wt.%. The melts are depleted in HREE and have high Th/U ratios (7.7–9.4). Study of melt inclusions using mineralogical thermobarometers showed that the scapolite-bearing granulite crystallized at ~1000 °C and ~15 kbar. This rock resulted, most likely, from the incongruent melting of carbonate-bearing biotite-quartz-plagioclase substrate in the lower crust, which was accompanied by the crystallization of garnet, clinopyroxene, sphene, plagioclase, and scapolite trapping microportions of acid melts as inclusions. The minerals crystallized not from melt but in its presence. High-Ca scapolite (Me67–69) crystallized instead of plagioclase when the melts reached high contents of CO2 (~1 wt.%) and Cl (≤ 0.8 wt.%) in the presence of CO2-rich fluid.