The Quaternary paleoclimate of the central Andes is poorly understood due to numerous discrepancies among the diverse proxy records that span this geographically and climatically complex region. The exact timing, duration and magnitude of wet and dry phases are seldom duplicated from one proxy type to another, and there have been few opportunities to compare climatic records from the same proxy along environmental gradients. Vegetation histories from fossil rodent middens provide one such opportunity on the Pacific slope of the Andes. We previously reported a vegetation history from the upper margin (2400–3000 m) of the absolute desert in the central Atacama Desert of northern Chile. That record identified a distinct wet phase that peaked between 11.8 and 10.5 ka, when steppe grasses and other upland elements expanded as much as 1000 m downslope, and a secondary wet period during the middle to late Holocene (7.1–3.5 ka). The latter wet phase remains controversial and is not as readily apparent in our low-elevation midden record. We thus sought to replicate both phases in a midden record from the mid-elevations (3100–3300 m) of the arid prepuna, where slight precipitation increases would be amplified. Midden records from these elevations identify conditions wetter than today at 13.5–9.6, 7.6–6.3, 4.4–3.2 and possibly 1.8–1.2 ka. Dry phases occurred at 9.4–8.4 ka and possibly at ca. 5.1 ka. Present floras and modern hyperarid conditions were established after 3.2 ka. The records from the two elevational bands generally match with some important differences. These differences could reflect both the discontinuous aspect of the midden record and the episodic nature of precipitation and plant establishment in this hyperarid desert.