The deep-time dynamics of coupled socio-ecological systems at different spatial scales is viewed as a key framework to understand trends and mechanisms that have led to the Anthropocene. By integrating archeological and paleoenvironmental records, we test the hypothesis that Chilean societies progressively escalated their capacity to shape national biophysical systems as socio-cultural complexity and pressures on natural resources increased over the last three millennia. We demonstrate that Pre-Columbian societies intentionally transformed Chile’s northern and central regions by continuously adjusting socio-cultural practices and/or incorporating technologies that guaranteed resource access and social wealth. The fact that past human activities led to cumulative impacts on diverse biophysical processes, not only contradicts the notion of pristine pre-Industrial Revolution landscapes, but suggests that the Anthropocene derives from long-term processes that have operated uninterruptedly since Pre-Columbian times. Moreover, our synthesis suggests that most of present-day symptoms that describe the Anthropocene are rooted in pre-Columbian processes that scaled up in intensity over the last 3000 years, accelerating after the Spanish colonization and, more intensely, in recent decades. The most striking trend is the observed coevolution between the intensity of metallurgy and heavy-metal anthropogenic emissions. This entails that the Anthropocene cannot be viewed as a universal imprint of human actions that has arisen as an exclusive consequence of modern industrial societies. In the Chilean case, this phenomenon is intrinsically tied to historically and geographically diverse configurations in society-environment feedback relationships. Taken collectively with other case studies, the patterns revealed here could contribute to the discussion about how the Anthropocene is defined globally, in terms of chronology, stratigraphic markers and attributes. Furthermore, this deep-time narrative can potentially become a science-based instrument to shape better-informed discourses about the socio-environmental history in Chile. More importantly, however, this research provides crucial “baselines” to delineate safe operating spaces for future socio-ecological systems.