Cratons, the ancient nuclei of continents that have been stable for billions of years, are underlain by keels of lithosphere with strongly melt-depleted compositions(1,2). These cratonic keels may have formed either from partial melting in a mantle-plume environment(3,4), or alternatively by melting at shallow depths in a subduction zone, during the successive accretion of slabs of oceanic lithosphere(5). The stability of cratonic keels has been attributed to a pervasive state of near-neutral buoyancy-isopycnicity-created by offsetting thermal and compositional effects on density(6). However, it is unclear how an isopycnic state can be sustained over geological time(2). Here we simulate the evolution of a simplified southern African cratonic keel, initiated in either a hot-plume or a cold-slab environment, over 3 billion years, using a numerical model that incorporates secular cooling of the mantle, coupled with gradual loss of radiogenic heating in the lithosphere. We find that the simulation that starts from a cold-slab environment best explains the subsidence history of the southern African craton(7). However, irrespective of how the cratonic keel formed, we find that the isopycnic state is inherently ephemeral: a cratonic keel that is approximately isopycnic under present conditions was more, or less, buoyant in the geologic past.