Carbon isotope compositions and the distribution of nitrogen and hydrogen in diamonds from 18 eclogites from Nurbinskaya kimberlites were studied in situ in polished plates. Cathodoluminescence images show that most of the diamonds have complex growth structures with distinctive core, intermediate and rim zones. In some diamonds the cores display dissolution features, and intermediate growth zones are separated from the cores by narrow rounded oscillatory zones. At least three crystals show interrupted multistage diamond growth; variations in δ13C of 2–3‰ occur across the contacts between distinct zones. Generally, δ13C within the diamond cores varies only by 1–2‰, in rare cases up to 3.3‰. δ13C values are usually lower in the intermediate zones and drop further towards the rims by up to 3‰. High-resolution SIMS profiles show that variations in δ13C across the diamond growth zones are sharp with no evidence of diffusive relaxation. Diamonds with predominantly tangential octahedral growth have a wide range in δ13C from − 15.2‰ up to 9.0‰ (± 0.4‰), and their nitrogen (N) contents vary between 30 and 1500 at. ppm. Six diamonds show little internal variation along the isotopic profiles with changes in δ13C of only 0.3–0.9‰ around mean values ranging from − 6‰ to − 3‰. Five crystals are isotopically heavy, with relatively homogeneous δ13C up to 9‰. FTIR data show markedly different N concentrations and nitrogen aggregation states between major growth zones. This implies that the diamonds in eclogitic xenoliths from Nyurbinskaya pipe grew in multiple and interrupted growth events, probably from fluids enriched in K and H. The wide variations of δ13C in the studied eclogitic diamonds and identification of their anomalously positive δ13C values, combined with the wide range of high δ18O in garnets from the diamondiferous xenoliths of the Nyurbinskaya pipe, which are mostly outside of the mantle range, suggest a crustal contribution to the parental mantle-related fluids forming diamonds in these xenoliths and indicate the complex metasomatic evolution of the lithospheric mantle beneath the Nakynsky kimberlite field.