These data comprise a downcore record (PEX19-01) of plant wax n-alkanes (concentration and compound-specific δ2H and δ13C isotopes) from 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. The lake covers an area of 0.02 km² with a maximum water depth of approximately 5 meters. Characterized as oligotrophic, slightly acidic, and monomictic, Lake Peixão's settings and location present an ideal setting for paleoenvironmental studies between Atlantic and Mediterranean-influenced climates. Sediment cores were collected at a depth of about 4 meters during a field campaign from June 10 to June 14, 2019, using a UWITEC© piston coring system from a floating platform, and a short core (PEX15-01C; 1.23 m long) using a UWITEC gravity coring system (see Moreno et al., 2023). According to the age model by Hernández et al., 2023, the studied section of the sediment core (upper 120 cm) spans the last 2000 years with a mean resolution of 30 ± 10 years for n-alkane samples.This study aims to reconstruct past vegetation and climate dynamics in western Iberia and to address the lack of long-term climate data. It focuses on understanding the interactions between Mediterranean and Atlantic influences on Western Iberia during key climatic periods such as the Roman Period, Early Middle Ages, Medieval Climate Anomaly, Little Ice Age, and the Industrial Era to the present day. This knowledge is crucial for predicting future climate scenarios and understanding the adaptive responses of alpine ecosystems to climatic variability.The sediment samples were collected every 2 cm, resulting in 60 samples weighing between 0.4 and 0.6 grams each. 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 (δ13C n-alk and δ2H n-alk) were conducted using gas chromatography-isotope ratio mass spectrometry (GC-IRMS) at MARUM, University of Bremen, Germany (see Santos et al., 2022).