The evolution of the planetary interior during plate tectonics is controlled by slow convection within the mantle. Global-scale geochemical differences across the upper mantle are known, but how they are preserved during convection has not been adequately explained. We demonstrate that the geographic patterns of chemical variations around the Earth's mantle endure as a direct result of whole-mantle convection within largely isolated cells defined by subducting plates. New 3D spherical numerical models embedded with the latest geological paleo-tectonic reconstructions and ground-truthed with new Hf-Nd isotope data, suggest that uppermost mantle at one location (e.g. under Indian Ocean) circulates down to the core-mantle boundary (CMB), but returns within ≥100 Myrs via large-scale convection to its approximate starting location. Modelled tracers pool at the CMB but do not disperse ubiquitously around it. Similarly, mantle beneath the Pacific does not spread to surrounding regions of the planet. The models fit global patterns of isotope data and may explain features such as the DUPAL anomaly and long-standing differences between Indian and Pacific Ocean crust. Indeed, the geochemical data suggests this mode of convection could have influenced the evolution of mantle composition since 550 Ma and potentially since the onset of plate tectonics.