The global distribution of late Pliocene soils and lakes has been reconstructed using a synthesis of geological data. These reconstructions are then used as boundary conditions for the Hadley Centre General Circulation Model (HadCM3) and the BIOME4 mechanistic vegetation model. By combining our novel soil and lake reconstructions with a fully coupled climate model we are able to explore the feedbacks of soils and lakes on the climate of the late Pliocene. Our experiments reveal regionally confined changes of local climate and vegetation in response to the new boundary conditions. The addition of late Pliocene soils has the largest influence on surface air temperatures, with notable increases in Australia, the southern part of northern Africa and in Asia. The inclusion of late Pliocene lakes increases precipitation in central Africa and at the locations of lakes in the Northern Hemisphere. When combined, the feedbacks on climate from late Pliocene lakes and soils improve the data to model fit in western North America and the southern part of northern Africa.