Crustal structure was derived from EarthScope Idaho-Oregon (IDOR) controlled-source seismic data across the Precambrian continental margin in the Idaho and Oregon region of the U.S. Cordillera. Refraction and wide-angle reflection traveltimes were inverted to derive a seismic velocity model that constrains the contact between oceanic accreted terranes and craton. The seismic data reveal that the boundary is a near-vertical, through-going feature of the crust, represented by the transpressional western Idaho shear zone (WISZ). The WISZ separates crust with different seismic velocities at all depths, implying a contrast in lithology, and extends to an ∼7 km offset of the Moho. The thinner, ∼32-km-thick accreted terrane crust to the west is characterized by faster seismic velocities that correspond to an intermediate composition. We interpret a high-velocity layer below a high-amplitude seismic reflection as mafic magmatic underplating associated with the feeder system of the Columbia River Basalts. The cratonic crust east of the WISZ is 37–40 km thick, with a felsic composition to ∼29 km subsurface depth, underlain by an intermediate-composition layer above the Moho. The strong contrasts in lithology and crustal thickness across the WISZ have influenced subsequent magmatism and extension in the region. The northwestern extent of the Archean Grouse Creek cratonic block beneath the Atlanta lobe of the Idaho batholith is interpreted based on continuity of crustal architecture in the seismic model. The velocity structure and crustal thickness east of the WISZ are consistent with the Atlanta lobe melting within a thickened crust.