The evolution of land plants during the Palaeozoic Era transformed Earth’s biosphere 1. Because the Earth's surface and interior are linked by tectonic processes, the linked evolution of the biosphere and sedimentary rocks should be recorded as a near-contemporary shift in the composition of the continental crust. To test this hypothesis, we assessed the isotopic signatures of zircon formed at subduction zones where marine sediments are transported into the mantle 2,3, thereby recording interactions between surface environments and the deep Earth. Using oxygen and lutetium-hafnium isotopes of magmatic zircon that respectively track surface weathering (time-independent) 4 and radiogenic decay (time-dependent) 5, we find a correlation in the composition of continental crust after 430 Myr ago, which is coeval with the onset of enhanced complexity and stability in sedimentary systems related to the evolution of vascular plants. The expansion of terrestrial vegetation brought channelled sand-bed and meandering rivers, muddy floodplains, and thicker soils, lengthening the duration of weathering before final marine deposition 6,7. Collectively, our results suggest that the evolution of vascular plants coupled the degree of weathering and timescales of sediment routing to depositional basins where they were subsequently subducted and melted. The late Palaeozoic isotopic shift of zircon indicates that the greening of the continents was recorded in the deep Earth.