Grasslands are one of the world's most extensive terrestrial biomes and are central to the survival of herders, their livestock and diverse communities of large wild mammals(1-3). In Africa, tropical soils are predominantly nutrient-limited(4-)(6) but productive grassy patches in wooded grassland savannah ecosystems(2)(,4) grow on fertile soils created by geologic and edaphic factors, megafauna, fire and termites(4-6). Mobile pastoralists also create soil-fertility hotspots by penning their herds at night, which concentrates excrement-and thus nutrients-from grazing of the surrounding savannahs(7-11). Historical anthropogenic hotspots produce high-quality forage, attract wildlife and increase spatial heterogeneity in African savannahs(4,)(12-15). Archaeological research suggests this effect extends back at least 1,000 years(16-19) but little is known about nutrient persistence at millennial scales. Here we use chemical, isotopic and sedimentary analyses to show high nutrient and N-15 enrichment in on-site degraded dung deposits relative to off-site soils at five Pastoral Neolithic(20) sites (radiocarbon dated to between 3,700 and 1,550 calibrated years before present (cal. BP)). This study demonstrates the longevity of nutrient hotspots and the long-term legacy of ancient herders, whose settlements enriched and diversified African savannah landscapes over three millennia.