This dataset contains the concentration and relative abundance of branched glycerol dialkyl glycerol tetraethers (brGDGTs) components, along with Methylation of Branched Tetraethers (MBT'5Me), Cyclisation of Branched Tetraethers (CBT'), isomer ratio of 6-methyl branched glycerol dialkyl glycerol tetraethers (IR6Me) and Isoprenoid acyclic glycerol dialkyl glycerol tetraether/Crenarchaeol ratio (isoGDGT-0/Cren), for the sedimentary record of Lago Grande di Monticchio (Italy) covering the last 12,900 years. The analysis was performed by a double microwave extraction at 70°C with dichloromethane (DCM)-methanol (MeOH) mixture (3:1, v/v), filtered on a solid-phase extraction (SPE) cartridge and then separated into polar and apolar fractions on a silica column with a hexane-DCM (1:1, v/v) and DMC-MeOH (1:1, v/v) mixtures, respectively. Samples were then analysed by high-performance liquid chromatography with mass spectrometry (HPLC-MS) in hexane-propanol (98.2:0.2, v/v). Ions in selected ion monitoring (SIM) are detected for mass-to-change ratios according to Hopmans et al. (2016, doi: 10.1016/j.orggeochem.2015.12.006). The data table also contains the quantitative climate reconstructions inferred from brGDGTs (mean annual temperature and mean temperature of months above freezing) from four different calibrations (linear and multiple regression and Bayesian calibration; Martínez-Sosa and Tierney, 2019; Raberg et al. 2021; De Jonge et al. 2014; Bauersachs et al. 2024), and the pH reconstruction based on the calibration of Russel et al. (2018).