Soils are key to ecosystems and human societies, and their critical importance requires a better understanding of how they evolve through time. However, identifying the role of natural climate change versus human activity (e.g. agriculture) on soil evolution is difficult. Here we show that for most of the past 12,300 years soil erosion and development were impacted differently by natural climate variability, as recorded by sediments deposited in Lake Dojran (Macedonia/Greece): short-lived ( < 1,000 years) climatic shifts had no effect on soil development but impacted soil erosion. This decoupling disappeared between 3,500 and 3,100 years ago, when the sedimentary record suggests an unprecedented erosion event associated with the development of agriculture in the region. Our results show unambiguously how differently soils evolved under natural climate variability (between 12,300 and 3,500 years ago) and later in response to intensifying human impact. The transition from natural to anthropogenic landscape started just before, or at, the onset of the Greek ‘Dark Ages’ (~3,200 cal yr BP). This could represent the earliest recorded sign of a negative feedback between civilization and environmental impact, where the development of agriculture impacted soil resources, which in turn resulted in a slowdown of civilization expansion.