Polycrystalline diamond aggregates (boart, framesites, diamondites) have been widely studied but their origin is poorly understood. We report the results of a study in situ of two polished fragments of fine-grained (40–400 μm size of individual diamond grains) dense polycrystalline diamond aggregates from the Mir pipe containing visible multiple interstitial garnet inclusions. They were analyzed for major and trace elements of inclusions and one of them — for δ13C and N abundance and isotopic composition of host diamonds. These aggregates are classified as variety IX by Orlov (1977). No cavities were observed in these samples. Sixty two irregular garnet grains and one clinopyroxene inclusion were detected and analyzed in sample Mr 832. Garnets are homogeneous within single grains but variable in Mg# [100Mg/(Mg + Fe)] from 60 up to 87 and CaO contents (3.3–5.3 wt.%) among grains with a trend to negative correlation. Low Cr (550–640 ppm) confirms eclogitic (E-type) paragenesis. High Na2O contents (5.2 wt.%) of a single pyroxene inclusion are additional evidence of eclogitic nature of this sample. Wide variations in trace elements (ppm) are characteristic for garnet grains: Sr (2.7–25.6), Y (9.7–14.1), Zr (15.6–38.7) and positive Eu anomaly is present. The δ13C of diamonds within studied sample is variable (− 6.4 ÷− 9.8 ‰) as well as N abundance (75–1150 ppm) and δ15N − 27, − 38, − 58 ‰. The second peridotitic (U/P-type) sample Mr 838 contains eight inclusions of Mg-rich Cr-pyropes (Mg# ~ 85, Cr2O3 3.2–3.4 wt.%) and magnesite inclusion with 4.35 wt.% FeO and 1.73 wt.% CaO. Trace element content in pyropes is relatively uniform (ppm): Sr (0.4–1.6), Y (13.2–13.4) and Zr (13.0). We conclude that heterogeneous distribution of the trace elements among garnet grains in Mr 832 and magnesite presence in Mr 838 are indicative of the effects of mantle metasomatism and rapid crystallization shortly before the eruption of the kimberlite.