This dataset contains compound-specific hydrogen (δ²H) and carbon (δ¹³C) isotope compositions and concentrations of plant wax n-alkanes from the PEX19-01 sediment record of Lake Peixão (40°20'35'' N, 7°36'19'' W), a small alpine lake located at 1677 meters above sea level in the Serra da Estrela Mountain, Portugal. Sediment cores were retrieved in June 2019 using a UWITEC piston coring system (Hernández et al., 2023). We adopt the age-depth model published by Hernández et al. (2023), which indicates continuous sedimentation over the past ~11,100 years. We present concentrations and compound-specific hydrogen (δ²H n-alk) and carbon (δ¹³C n-alk) isotope compositions of plant-wax n-alkanes from 75 sediment samples between 149 and 730 cm depth (~2.2–11.1 cal. ka BP), sub-sampled at variable intervals (2, 4, 8, 12, 16, and 20 cm) to optimise temporal resolution and stratigraphic coverage. These data extend the record previously published by Santos et al. (2024), which covers the uppermost 149 cm (~0–2.2 cal. ka BP). Plant-wax n-alkanes were extracted and analyzed at the BioGeoChemistry Lab, IPMA in Lisbon, Portugal. The total lipid extracts underwent various purification and analysis steps, including ultrasonic bath extraction, hydrolysis with potassium hydroxide in methanol, and separation using silica gel columns. Concentrations were measured using gas chromatography with flame ionization detection (GC-FID). Compound-specific isotope analyses were conducted using gas chromatography-isotope ratio mass spectrometry (GC-IRMS) at MARUM, University of Bremen, Germany (see Santos et al., 2022). The dataset was generated to reconstruct past hydroclimate and vegetation dynamics in Western Iberia.