The shallow East Siberian Arctic Shelf (ESAS) shows high methane concentration in seawater; however, methane oxidation processes for the ESAS are poorly constrained. Here, we examined porewater geochemical profiles, microbial lipids, and their carbon isotope compositions in multiple sediment cores to explore molecular-isotopic diagnostics of microbial methane oxidation in the outer Laptev Sea. There was covariation between methane and sulfate profiles in only one core in the studied upper 20 cm. Across all cores, concentrations of microbial fatty acids (C₁₂–C₁₈) decreased sharply below the surface sediment with carbon isotope compositions (δ¹³C) ranging from −31 to −20‰. Notably, anaerobic methane oxidizing archaea (ANME)-derived lipid biomarkers, e.g., 2,6,10,15,19-pentamethylicosane, archaeal and hydroxyarchaeol, were absent or below detection limits, indicating that anaerobic methane oxidation (AOM) was not a dominant process in the studied sediment. However, the tetraether-based Methane Index increased from 0.03 to 0.8 in the core where sulfate and methane covaried, implying either a developing AOM microbial community with presently low activity or an episodic AOM event occurring within the past decades to a century. In contrast, hop-17(21)-ene was present throughout the cores, exhibiting strong ¹³C depletion, with values ranging from −66.1 to −44.0‰. The concentration and δ¹³C values of hop-17(21)-ene were distinct from the terrestrially-derived nC₃₁ alkane, which showed relatively constant δ¹³C values of −34.9 ± 1.1‰. This suggests that hop-17(21)-ene in the sediments is primarily derived from marine microbes. Given the oxic seawater in this system (< 60 m), the ¹³C-depleted hop-17(21)-ene likely reflects aerobic methane oxidation (AeOM) occurring in the water column and/or in surface sediments. AeOM may play a significant role in regulating methane in this subsea permafrost seepage system.