Migmatites and granitic-gneisses exhumed in Archean to Phanerozoic segments are former partially molten crustal roots, display typical domes structures ranging in size from kilometres to decakilometres, and are often interpreted as resulting from the development of diapiric or convective gravitational instabilities. In previous work (part I), we determined various regimes of gravity-driven segregation, by considering a thick continental crust heated from below and containing melt related heterogeneities. These heterogeneities, represented by inclusions of distinct densities and viscosities with respect to the ambient partially molten material, can be entrained into convection cells (in the ‘suspension’ and ‘layering’ regimes) and/or accumulate as clusters (in the ‘layering’ and ‘diapirism’ regimes). Here we further investigate the specific conditions that allow for the formation and preservation of domes resulting from diapirism at the top of convective cells. We show that both the cessation of basal heating and the freezing of the buoyant inclusions density favour their stacking and preservation at ca. 15 km depth, within about 10 Myr. The buoyant inclusions form domes, 5–20 km in size, that also record several convective cycles at velocities ranging from 0.5–4 cm yr−1. 3-D models demonstrate their radial geometrical nature. The influence of the size and concentration of the inclusions is also assessed, complementing the characteristics of crustal heterogeneity in driving its differentiation and the formation of migmatite domes.