Abstract Major flood basalt emplacement events can dramatically alter the composition of the sub-continental lithospheric mantle (SCLM). The Siberian craton experienced one of the largest flood basalt events preserved in the geologic record — eruption of the Permo-Triassic Siberian flood basalts (SFB) at ~ 250 Myr in response to upwelling of a deep-rooted mantle plume beneath the Siberian SCLM. Here, we present helium isotope ( 3 He/ 4 He) and concentration data for petrologically-distinct suites of peridotitic xenoliths recovered from two temporally-separated kimberlites: the 360 Ma Udachnaya and 160 Ma Obnazhennaya pipes, which erupted through the Siberian SCLM and bracket the eruption of the SFB. Measured 3 He/ 4 He ratios span a range from 0.1 to 9.8 R A (where R A = air 3 He/ 4 He) and fall into two distinct groups: 1) predominantly radiogenic pre-plume Udachnaya samples (mean clinopyroxene 3 He/ 4 He = 0.41 ± 0.30 R A (1σ); n = 7 excluding 1 outlier), and 2) ‘mantle-like’ post plume Obnazhennaya samples (mean clinopyroxene 3 He/ 4 He = 4.20 ± 0.90 R A (1σ); n = 5 excluding 1 outlier). Olivine separates from both kimberlite pipes tend to have higher 3 He/ 4 He than clinopyroxenes (or garnet). Helium contents in Udachnaya samples ([He] = 0.13–1.35 μcm 3 STP/g; n = 6) overlap with those of Obnazhennaya ([He] = 0.05–1.58 μcm 3 STP/g; n = 10), but extend to significantly higher values in some instances ([He] = 49–349 μcm 3 STP/g; n = 4). Uranium and thorium contents are also reported for the crushed material from which He was extracted in order to evaluate the potential for He migration from the mineral matrix to fluid inclusions. The wide range in He content, together with consistently radiogenic He-isotope values in Udachnaya peridotites suggests that crustal-derived fluids have incongruently metasomatized segments of the Siberian SCLM, whereas high 3 He/ 4 He values in Obnazhennaya peridotites show that this section of the SCLM has been overprinted by Permo-Triassic (plume-derived) basaltic fluids. Indeed, the stark contrast between pre- and post-plume 3 He/ 4 He ratios in peridotite xenoliths highlights the potentially powerful utility of He-isotopes for differentiating between various types of metasomatism (i.e., crustal versus basaltic fluids).