A 370,000-year paleoecological history of fire spanning four glacial cycles provides evidence of plant migration in response to Andean climate change. Charcoal, an indicator of fire, is only occasionally observed in this record, whereas it is ubiquitous in Holocene-aged Andean records. Fire is a transformative agent in Amazonian and Andean vegetation but is shown to be rare in nature. As humans promote fire, fire-free areas become microrefugia for fire-sensitive species. A distinction is drawn between microrefugia resulting from fire-free zones and those caused by unusual climatic conditions. The importance of this distinction lies in the lack of warmer-than-modern microrefugia aiding upslope migration in response to warming, whereas fire-free microrefugia support tree species above modern tree line or in areas of Amazonia least used by humans. The synergy between fire, deforestation, and climate change could promote a state-change in the ecosystem, one where new microrefugia would be needed to maintain biodiversity. Past tipping points are identified to have occurred within ca. 1°C–1.5°C of modern conditions. The recent climatic instability in both Amazonia and the Andes is viewed in the context of ecological flickering, while the drought-induced and fire-induced tree mortality are aspects of critical slowing down; both possibly portending an imminent tipping point.