Leaf cuticular waxes are one of the most important environment-plant interaction structural systems that enable desert plants to withstand extreme climatic conditions. We present a long chain n-alkyl lipids study in fresh plant leaves and rodent palaeomiddens collected along an elevational gradient in the south-central Atacama Desert of Chile, covering six different vegetation belts: Steppe (4500-4000 m asl), Puna (4000-3300 m asl), pre-Puna (3300-2400 m asl), Absolute Desert (2400-1000 m asl) and Coastal Desert (1000-0 m asl). The 28 rodent palaeomiddens analyzed from Quebrada Incahuasi (25.6 °S, 3600 m asl) span the last 17,000 years. Modern-day distribution of long-chain n-alkanes and n-alkanoic acids varies among the dominant plant associations of the Atacama Desert. These plants show a species-specific chemotaxonomy linked to the climatic conditions. Furthermore, differences in average chain length (ACL) and carbon preference index (CPI) suggest that these plant communities are highly adapted to extreme environmental conditions. The sum of leaf wax n-alkanes was highest under wet conditions, while n-alkanoic acids (between n-C24 and n-C28) increased with hyperaridity. Similarly, analysis of n-alkane time series from palaeomiddens showed that the greatest changes in leaf wax n-alkane distributions (ACL and CPI) corresponded to the greatest increases in moisture during the Central Andean Pluvial Event (CAPE; between 18 and 9 ka cal BP) and the Late Holocene. The shift in the palaeomidden n-alkane distributions is corroborated by the relative abundance of rainfall-dependent extra-local taxa. This is the first study to report leaf wax content obtained from ancient rodent middens, and shows promising results as a robust hydroclimate proxy for the Atacama Desert region. •n-Alkyl leaf waxes obtained from ancient Atacama rodent middens can be used to infer past climate change.•An elevational survey of leaf cuticular waxes in the Atacama Deserts shows that their composition varies at the ecosystem scale.•Ancient middens reveal significant responses in n-alkane composition and plant macrofossils to millennial-scale hydroclimate shifts over the past 17,000 years.•Our reconstruction traces the Central Andean Pluvial Events and shows that paleomiddens are a valuable source of leaf wax.