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These datasets contain compound-specific stable carbon isotope values (δ¹³C, ‰ vs. VPDB) for a range of core lipids (CLs) and intact polar lipids (IPLs) of diverse microbial origin, derived from total lipid extracts (TLEs) of hydrothermally influenced marine sediments. The sediment cores utilized within this study were retrieved using the ALVIN submersible during the R/V Atlantis research cruises AT42-05 (Nov. 15-29, 2018) and AT37-06 (Dec. 09-27, 2016) targeting the southern Guaymas Basin spreading center (Core IDs: 4869-3, 4870-28, 4871-28; 4992-14 & 5000-9) and an off-axis Central Seep site on the northwestern flanks (Core ID: 4867-3).