The dataset comprises alkanoic acids composition data that was obtained on sediment samples from sub-Antarctic South Georgia. The sediments were collected from a range of different sites, including lakes, peat deposits, a marine inlet and a fjord during RV Polarstern expedition PS81 in 2013. Prior to the geochemical analyses reported here, the sediments were freeze-dried and ground. More details on the study sites, sampling and data evaluation can be found in Berg et al. (submitted manuscript).Alkyl lipid biomarkers were extracted by accelerated solvent extraction (ASE 300, Thermo, USA) with dichloromethane and methanol (DCM, MeOH; 9:1, v/v at 120°C, 75 bar) (cores Co1305, PS81/283, and Co1308) or via consecutive ultrasonication in DCM:Hexan (1:1), MeOH:DCM (1:1) and MeOH (core Co1306 and the peat and soil samples).The total lipid extract (TLE) was saponified with 0.5 M KOH in MeOH and water (9:1, v/v) at 80°C for 2 h. Neutral lipids (NL) were extracted from the TLE with dichloromethane by liquid-liquid phase separation. To purify alkanoic acids, the remaining TLE was acidified to pH 1 and acids were extracted from the TLE with dichloromethane by liquid-liquid phase separation. Prior to analysis by gas chromatography (GC, Agilent 7890B, Agilent Technologies, USA) equipped with a flame ionization detector (FID), alkanoic acids were converted to methyl ester derivatives. Alkanoic acids were identified and quantified against authentic external standards. Concentrations are given as fractional abundances for the compound class.