During the Pleistocene-Holocene transition, the dominant mammoth steppe ecosystem across northern Eurasia vanished, in parallel with megafauna extinctions. However, plant extinction patterns are rarely detected due to lack of identifiable fossil records. Here, we introduce a method for detection of plant taxa loss at regional (extirpation) to potentially global scale (extinction) and their causes, as determined from ancient plant DNA metabarcoding in sediment cores (sedaDNA) from lakes in Siberia and Alaska over the past 28,000 years. Overall, potential plant extinctions track changes in temperature, in vegetation, and in megafauna extinctions at the Pleistocene-Holocene transition. Estimated potential plant extinction rates were 1.7-5.9 extinctions per million species years (E/MSY), above background extinction rates but below modern estimates. Major potential plant extinction events were detected around 17,000 and 9000 years ago which lag maximum vegetation turnover. Our results indicate that herbaceous taxa and taxa contributing less to beta diversity are more vulnerable to extinction. While the robustness of the estimates will increase as DNA reference libraries and ancient sedaDNA data expand, the available data support that plants are more resilient to environmental changes than mammals.