Rifting of continental crust initiates faults that are commonly influenced by pre-existing structures. We document newly identified faults cutting Precambrian units in the interior of the NE Brazilian margin to assess the effects of structural inheritance on both rift geometry and fault architecture. Stratigraphic and structural data indicate that the faults were active in the main phase of rifting of Gondwana. The influence of pre-existing structures on the Mesozoic rift faulting is scale dependent. Regionally, the faults trend parallel to subvertical, crustal-scale Brasiliano (c. 750–540 Ma) shear zones. Mylonitic foliations and broadly distributed low strain in the lower crust indicated by shear-wave splitting controlled the overall orientation and kinematics of the rift faults. However, outcrop observations of the faults show that at scales up to hundreds of metres, mylonitic foliations have little influence on fault architectures. Faults cross-cut shear zones and do not commonly utilize foliation planes as shear fractures. Instead, slip zones and fractures have a range of orientations that form acute angles to the local foliation orientation. This observation explains the range of focal mechanisms associated with seismicity that coincides with ancient shear zones in intra-continental areas.