The Eastern European Alps boasts highly biodiverse ecosystems and a rich archaeological history. However, there is limited research on the enduring impacts of historical climate change and human activities on plant biodiversity in this region. Using sedimentary ancient DNA, we reconstructed plant and animal dynamics from 8500 years before present (ka BP) around Großer Winterleitensee (Zirbitzkogel, Austria). Variable intensities of human activities since the Middle Bronze Age (~3.5 ka BP) facilitated the persistence of biodiverse Alpine meadow communities and lowered timberlines below their natural limit. Since the end of the Bronze Age (~2.8 ka BP), human activities, particularly pasturing, and increasing temperatures, emerged as significant drivers of plant community dynamics. The introduction of sheep ( Ovis aries ) did not reduce wild mammal presence, including red deer ( Cervus elaphus ), hare ( Lepus ), European mole ( Talpa europaea ), bank vole ( Myodes glareolus ), and short-tailed field vole ( Microtus agrestis ). During the High & Late Mediaeval Period, (~1150–450 BP), cattle ( Bos taurus ) and horses ( Equus caballus ) became the dominant domesticates, while all wild mammals except the short-tailed field vole and Eurasian water shrew ( Neomys fodiens ) declined or even disappeared. These changes are also accompanied by a significant transformation of plant community structure. The ability to determine both plant responses and animal drivers from the same palaeolimnological sequence vastly improves our ability to partition causes of vegetation change over the Holocene. Here, we reveal that plant biodiversity is maintained or increased by moderate cattle grazing. Therefore, non-intensive domesticated stock grazing is essential for maintaining diverse Alpine meadows.