The Barreirinhas pull-apart system encompasses marginal basins in divergent and transform margin segments in the central sector of the Brazilian Equatorial Margin and its African conjugate counterpart. This ancient pull-apart system evolved through transtensional strike-slip motion within a highly heterogeneous crystalline basement affected by multiple rift phases. The geometry and development of pull-apart structural elements during the final rifting phase before continental breakup and the mechanisms and extent to which they were influenced by preexisting crustal heterogeneities are comprehensively addressed using an extensive database of potential field (magnetic and gravity) and 2D seismic reflection data. We also assess the lithospheric thermomechanical conditions and their influence on transtensional extension throughout Curie Point Depth, Heat Flow, and Moho depth, derived from potential field data and published seismological models. Plate reconstruction of Brazilian and African equatorial margins based on gravity patterns and comparison with sandbox analog models allow a 3D synoptic model to reveal the Barreirinhas pull-apart system evolution during the Equatorial Atlantic opening. During the rift phase I, the location of major grabens was controlled by favorably oriented Neoproterozoic shear zones, while the cooler, stronger, and thicker crust beneath cratonic areas formed the western barrier to strike-slip rift activity during rift phase II. This same geological domain anchored the onset of the pull-apart system in the last rift phase III, whose principal displacement zones developed along the extensive oceanic fracture zones linked by sigmoidal fault systems. Toward the end of the rift phase, a large asymmetric lozangle to a lazy-Z-shaped, pull-apart basin developed above low overlapping ∼90°, releasing stepover in oblique transtensional strike-slip motion.