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Differentiation of the continental crust is the result of complex interactions between a large number of processes, which govern partial melting of the deep crust, magma formation and segregation, and magma ascent to significantly higher crustal levels. The anatectic metasedimentary rocks exposed in the Southern Marginal Zone of the Limpopo Belt represent an unusually well‐exposed natural laboratory where the portion of these processes that operate in the deep crust can be directly investigated in the field. The formation of these migmatites occurred via absent incongruent melting reactions involving biotite, which produced cm‐ to m‐scale, K2O‐poor garnet‐bearing stromatic leucosomes, with high Ca/Na ratios relative to their source rocks. Field investigation combined with geochemical analyses, and phase equilibrium modelling designed to investigate some aspects of disequilibrium partial melting show that the outcrop features and compositions of the leucosomes suggest several steps in their evolution: (1) Melting of a portion of the source, with restricted plagioclase availability due to kinetic controls, to produce a magma (melt + entrained peritectic minerals in variable proportions relative to melt); (2) Segregation of the magma at near peak metamorphic conditions into melt accumulation sites (MAS), also known as future leucosome; (3a) Re‐equilibration of the magma with a portion of the bounding mafic residuum via chemical diffusion (H2O, K2O), which triggers the co‐precipitation of quartz and plagioclase in the MAS; (3b) Extraction of melt‐dominated magma to higher crustal levels, leaving peritectic minerals entrained from the site of the melting reaction, and the minerals precipitated in the MASs to form the leucosome in the source. The key mechanism controlling this behaviour is the kinetically induced restriction of the amount of plagioclase available to the melting reaction. This results in elevated melt H2O and K2O and chemical potential gradient for these components across the leucosome/mafic residuum contact. The combination of all of these processes accurately explains the composition of the K2O‐poor leucosomes. These findings have important implications for our understanding of melt segregation in the lower crust and minimum melt residency time which, according to the chemical modelling, is <5 years. We demonstrate that in some migmatitic granulites, the leucosomes constitute a type of felsic refractory residuum, rather than evidence of failed magma extraction. This provides a new insight into the ways that source heterogeneity may control anatexis.