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The relationship between rifting and continental flood basalt eruptions is debated, and a control by mantle plume is commonly invoked for flood basalts production. In this work, we investigate the relationship between magmatism and rifting by studying the flood basalts erupted in Afar (4.5–0.6 Ma), known as the Stratoid and Gulf Series. We present new field observations and petrography, major and trace elements analyses and mineral chemistry of lavas collected during a regional campaign in Afar. The Series are characterized by E‐MORB magmatism and residual amphibole in the mantle source, consistent with the contribution of metasomatized sub‐continental lithospheric mantle during partial melting. Differences in garnet‐compatible elements indicate a shallower melting column for the oldest and youngest products (4.5–2.6 Ma Lower Stratoid Series; 1.1–0.6 Ma Gulf Series), and deeper for the products erupted at 2.6–1.1 Ma (Upper Stratoid Series). Incompatible element ratios (Th/Nb, Th/Zr) indicate a higher degree of partial melting for the Gulf with respect to the Upper Stratoid Series. Accordingly with independent geophysical and stratigraphic evidence, we explain our results with rift re‐localization: the Pliocene rift caused thinning of the lithosphere and the Lower Stratoid eruptions in Southern Afar, then the Pleistocene rift jumped to Central Afar under a less‐extended lithosphere, producing the Upper Stratoid and, subsequently, as stretching of the lithosphere localized, the Gulf Series formed. Our findings suggest that rift migration and localization can exert a fundamental control on the spatial variability and character of flood basalts without requiring variations on the activity of the mantle plume. Plain Language Summary: Afar is a volcanically active low‐lying area in Ethiopia, where the separation of the tectonic plates is breaking up the African continent and leading to the formation of new oceans (i.e., Red Sea, Gulf of Aden). It is therefore an excellent place to study the role of volcanism and related subsurface movements of magma during this transition from continent to ocean. In this work, we studied the Stratoid Series, a huge succession of basaltic lava flows covering much of the Afar depression, and the younger Afar Gulf Series lava flows, which were jointly erupted from 4.5 to 0.6 Ma. This study allows us to identify different mantle sources producing the magmas erupted during the breaking‐up process and to recognize two distinct episodes of "break‐up" in Afar. We interpret the process that guides the passage from one to the other and identify the "evolutionary stages" of the break‐up process toward what is going to be a new ocean. Key Points: Metasomatized, amphibole‐bearing lithospheric component in the mantle sources of the 4.5–0.6 Ma basaltic magmatism in AfarDeeper partial melting column for the Upper Stratoid Series mantle source with respect to the Lower Stratoid and the Gulf SeriesStratoid Series flood basalt volcanism related to rift jump of the Red Sea rift branch and not to a single magmatic event [ABSTRACT FROM AUTHOR]