ABSTRACTIn the past two decades, much has been learned about the late Quaternary climate history of the Atacama Desert with some details still unclear about the seasonality, timing and extent of wet and dry phases. Modern climate studies reveal that, far from exhibiting a unique pattern, seasonal precipitation originates from many sources and mechanisms. For the last 16 ka, we attempt to sort out these complexities in pollen records from four fossil rodent midden series spanning 22°–25°S in northern Chile. Widespread wet conditions prevailed during the late Pleistocene and early Holocene, particularly between 13 and 9 ka, evidenced by <400 m lowering of pollen zones (plant communities) compared to today. Regional differences in the timing and magnitude of this displacement may be related to the prevailing source (tropical/extra‐tropical) or mode (NNW/SE) of tropical precipitation through time. Wet conditions persisted well into the early Holocene, lasting ∼1–1.5 ka longer than previously suggested. The pollen record suggests extreme drying ∼8 ka, possibly associated with a northward shift of the Inter Tropical Convergence Zone, tracking minimum insolation values at subtropical latitudes during the austral summer. The establishment of conditions similar to today happened ∼4 ka. Copyright © 2017 John Wiley & Sons, Ltd.