Continental rifts are important sources of mantle carbon dioxide (CO2) emission into Earth’s atmosphere. Because deep carbon is stored for long periods in the lithospheric mantle, rift CO2 flux depends on lithospheric processes that control melt and volatile transport. The influence of compositional and thickness differences between Archaean and Proterozoic lithosphere on deep-carbon fluxes remains untested. Here we propose that displacement of carbon-enriched Tanzanian cratonic mantle concentrates deep carbon below parts of the East African Rift System. Sources and fluxes of CO2 and helium are examined over a 350-kilometre-long transect crossing the boundary between orogenic (Natron and Magadi basins) and cratonic (Balangida and Manyara basins) lithosphere from north to south. Areas of diffuse CO2 degassing exhibit increasing mantle CO2 flux and 3He/4He ratios as the rift transitions from Archaean (cratonic) to Proterozoic (orogenic) lithosphere. Active carbonatite magmatism also occurs near the craton edge. These data indicate that advection of the root of thick Archaean lithosphere laterally to the base of the much thinner adjacent Proterozoic lithosphere creates a zone of highly concentrated deep carbon. This mode of deep-carbon extraction may increase CO2 fluxes in some continental rifts, helping to control the production and location of carbonate-rich magmas.