This data file contains the total organic carbon (TOC) content and the distribution of isoprenoid and branched glycerol dialkyl glycerol tetraethers (isoGDGTs and brGDGTs, respectively) from the Padul palaeolake record (Padul-15-05 sediment core) covering the last 36-4.7 kyr. BrGDGTs-based indices (MBT'5ME and CBT') have been calculated and used for reconstructing paleoenvironmental conditions such as mean annual air temperature (MAAT), mean temperature of Months Above Freezing (MAF) and lake-pH. The identification of the IIIa'' isomer and calculation of the IIIa'' ratio have been used to evaluate the in-situ production in the water column of brGDGTs. The abundance of the isomer of crenarchaeol (%cren') relative to crenarchaeol evaluates the presence of other archaea than aquatic Thaumarchaeota. The composition of the brGDGTs in form of in the Padul palaeolake sedimentary record (triangles). The tetramethylated (Ia-c), pentamethylated (IIa-IIc and IIa'-IIc'), and hexamethylated (IIIa-IIIc and IIIa'-IIIc') brGDGTs are provided in order to compare with data reported from surface sediments of other lakes over the world.