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Magmatism plays a key role in accommodating and localizing extension during continental breakup. However, how the crustal magmatic systems evolve at the continental-ocean transition is poorly understood. We address these questions by studying the evolution of the magmatic system in the rift of Central Afar (Ethiopia), currently marking the transition from continental rifting to oceanic spreading. We focus on the voluminous and widespread Upper Stratoid Series (2.6–1.1 Ma) and the following Central Afar Gulf Series (1.1–0.6 Ma), the latter corresponding to localization of volcanism in narrow magmatic segments. We carried out the first systematic study of major and trace element mineral chemistry for these two Series and integrated it with geothermobarometry estimates and geochemical modeling, to reconstruct the evolution of the magmatic system architecture during rift localization. The Upper Stratoid magmas evolved by fractional crystallization in a melt-rich, moderately zoned, middle-lower crustal (10–18 km) magmatic system, from where they rose directly to the surface. Polybaric plagioclase convection and dissolution of a plagioclase-rich crystal mush is recorded in the phenocryst texture and chemistry. The Central Afar Gulf magmas evolved at similar depth in a more complex and dynamic storage system, with magma rising and mixing through multiple, relatively small, crystal-rich and interconnected reservoirs. Our study documents the transition during the continental breakup, from an overall stable and melt-rich magmatic system feeding the voluminous and homogeneous Upper Stratoid eruptions to a more dynamic, interconnected and crystal-rich situation feeding small-volume eruption while the rift localizes.