<p>Humans have been modifying ecosystems for millennia. By the start of the Holocene, approximately 11,500 years ago, human societies were influencing an estimated three-quarters of terrestrial ecosystems. In this Review, we focus on how advances in archaeology, biogeography, history and palaeoecology, combined with modelling techniques, are enabling researchers to evaluate long-term human influences on ecosystems across different spatial and temporal scales. We describe key methods for studying human transformations on past ecosystems, and explore how humans have shaped ecosystems across space and time. We outline ways that human societies have transformed global ecosystems with increasing intensity and diversity, driving accelerated rates of ecological change that often surpass natural variability. Processes such as species extinctions, introductions and range shifts have also altered patterns of biodiversity and ecosystem functions. Despite major advances in understanding human effects on ecosystems, important knowledge gaps remain. These gaps include information about novel ecosystems, hybrid cultural–natural ecosystems, accurate prediction of rates of change and chronological control of potential drivers of change. Addressing these gaps demands improved research methods and interdisciplinary approaches to better anticipate and mitigate future anthropogenic disturbances on global biodiversity.</p>