The dataset was used to map the spatial information of the subsurface to build an accurate representative stratigraphy for calculating the carbon storage of the initially degraded peats in a small valley system of the Alpine Foreland in Bavaria; the Loosbach valley at Pestenacker, an UNESCO world heritage site of Late Neolithic wetland occupation. In detail, we used geophysical prospection methods (Electromagnetic Induction and Electrical Resistivity Tomography) to map the distribution and thickness of peat deposits, and conducted direct push sensing and driving core drilling to ground-truth the geophysical data and to sample bulk material for subsequent carbon analysis in the laboratory.Electromagnetic induction (EMI) was measured with a CMD-Mini Explorer (GF Instruments s.r.o., Brno, Czech Republic) in May 2018 and June 2019. We used the vertical dipole (VDP) at coil spacings of 0.32 m (VDP1), 0.71 m (VDP2) and 1.18 m (VDP3). With the existing coil spacings, effective penetration depths of 0.5 m (VDP1), 1.0 m (VDP2) and 1.8 m (VDP3) could be achieved. According to the manufacturer, 70 % of the signal originate from above these depths. The EMI sensors measured the apparent electrical conductivity (ECa, in mS/m). Measurements were taken by carrying the instrument about 0.2 m above the ground while being directly connected to D-GPS (Leica GPS1200) for positioning. The acquisition rate was five measurements per second. Data quality was checked by measuring a reference line before and after each measurement. The maximum offset of the EMI values between the two time points was 1.5 mS/m. We corrected the data and removed the reference lines and single outliers.The data set contains the EMI data with an intercoil spacing of 0.71 m (VDP2) and 1.18 m (VDP3). The measured values of the VDP1 (coils spacing of 0.32 m) could not be used due to a high signal-to-noise ratio.The Electrical Resistivity Tomography (ERT) data were acquired by using a PC controlled DC resistivity meter system (RESECS, GeoServe, Kiel, Germany) in June 2019. We measured two transects with an electrode spacing 0.5 m. For both transects (transect A with a total length of 158 m, transect C with a total length of 103 m) we applied a Wenner alpha configuration. The coordinates and the height of the electrodes were measured with a D-GPS (Leica GPS1200).