This work studies and compares the main morphological, structural, and mineralogical features of 350 diamond crystals from the Karpinsky-I and 300 crystals of the Arkhangelskaya kimberlite pipes. The share of crystals of octahedral habit together with individual crystals of transitional forms with sheaf-like and splintery striation is higher in the Arkhangelskaya pipe and makes 15 %. The share of cuboids and tetrahexahedroids is higher in the Karpinsky-I pipe and stands at 14 %. The share of dodecahedroids in the Arkhangelskaya and Karpinsky-I pipes are 60 % and 50 %, respectively. The indicator role of the nitrogen-vacancy N3 center active in absorption and luminescence is shown. Crystals with the N3 absorption system have predominantly octahedral habit or dissolution forms derived from the octahedra. Their thermal history is the most complex. Absorption bands of the lowest-temperature hydrogen-containing defects (3050, 3144, 3154, 3188, 3310 cm−1, 1388, 1407, 1432, 1456, 1465, 1503, 1551, 1563 cm−1), are typical for crystals without N3 system, where in the absorption spectra nitrogen is in the form of low-temperature A and C defects. The above mentioned bands are registered in the spectra of 16 % and 42 % of crystals from the Arkhangelskaya and Karpinsky-I pipes, respectively. The diamond of the studied deposits is unique in the minimum temperature (duration) of natural annealing. Based on a set of features, three populations of crystals were distinguished, differing in growth conditions, post-growth, and thermal histories. The established regularities prove the multi-stage formation of diamond deposits in the north of the East European Platform and significant differences from the diamonds of the Western Cisurals. The results suggest the possibility of the existence of primary deposits dominated by diamonds from one of the identified populations.