Rooting depth is an ecosystem trait that determines the extent of soil development and carbon cycling. Recent hypotheses propose that human-induced changes to Earth’s biogeochemical cycles propagate deeply due to rooting depth changes from agricultural and climate-induced land cover changes. Yet, the lack of a global-scale quantification of rooting depth responses to human activity limits knowledge of hydrosphere-atmosphere-lithosphere feedbacks in the Anthropocene. Here we use land cover datasets to demonstrate that global rooting depths have become shallower in the Anthropocene, and are likely to become yet shallower this century. Specifically, globally averaged depths above which 99% of root biomass occurs (D99) are 8.7%, or 16 cm, shallower relative to those for potential vegetation. This net shallowing results from agricultural expansion truncating D99 by 82 cm, and woody encroachment linked to anthropogenic climate change extending D99 by 65 cm. Projected land cover scenarios in 2100 suggest further D99 shallowing of 63 to 72 cm, exceeding that experienced to date and suggesting that the pace of root shallowing will quicken in the coming century. Losses of Earth’s deepest roots—soil-forming agents—suggest unanticipated changes in fluxes of water, solutes, and carbon. Our work constrains rooting depth distributions for global models, allowing the land modeling community to explore cascading effects of rooting depth changes on water, carbon, and energy dynamics, and can guide design of field-based efforts to quantify deep anthropogenic influences. Understanding human influence on biota’s reach into Earth’s subsurface will improve predictions of interactive functioning of the biosphere, lithosphere, and hydrosphere.