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Human–environment interactions are a focus of interdisciplinary research in the high Andes, recently invigorated by sediment-core data from Lake Junín (Chinchaycocha). On the basis of these records, recent articles have argued that humans arrived in the Junín basin 13 thousand calibrated years ago (kya), set large-scale fires, and hunted Pleistocene megafauna to extinction. Declines in montane tree pollen beginning ~4 kya have been attributed to deforestation, camelid domestication, and agriculture on the high Andean puna. In this paper, we critically examine these arguments and contrast them with a compilation of archaeological data from the Lake Junín basin including 113 radiocarbon dates (12 unpublished), settlement patterns, camelid osteometry, macrobotanical remains, Inca period sites, and ethnographic and ethnohistoric descriptions of herding and farming. These data suggest that the earliest archaeological evidence for human occupation is not until ~11 kya, and there is no clear evidence for interaction with Pleistocene megafauna. Although the Junín basin is often cited as a center for camelid domestication in the middle Holocene, this claim remains tenuous, since osteometry struggles to distinguish wild and domestic camelids. Finally, ethnohistoric and ethnographic information offer no support for the argument that the basin was a "manufactured landscape" in the late Holocene. Moving forward, we recommend more careful consideration of (1) the mismatch of temporal resolution in paleoecological and archaeological chronologies, (2) the potential spatial mismatch in the catchment area of palaeoecological proxies and archaeological datasets, and (3) ambiguity in Sporormiella as a proxy for fauna and charcoal as a proxy for human activity. We suggest that future work on paleoecological proxies from 0.7 to 0.3 kya could be harnessed to build a comparative baseline, since these centuries saw large populations of humans and domesticated camelids near the lake. Our goal is to promote more robust reconstructions of human–environment interactions in the Lake Junín basin and elsewhere.