From west to east along the Sunda-Banda arc, convergence of the Indo-Australian plate transitions from subduction of oceanic lithosphere to arc-continent collision. This region of eastern Indonesia and Timor-Leste provides an opportunity for unraveling the processes that occur during collision between a continent and a volcanic arc, and it can be viewed as the temporal transition of this process along strike. We collected a range of complementary geological and geophysical data to place constraints on the geometry and history of arc-continent collision. Utilizing ∼4 yr of new broadband seismic data, we imaged the structure of the crust through the uppermost mantle. Ambient noise tomography shows velocity anomalies along strike and across the arc that are attributed to the inherited structure of the incoming and colliding Australian plate. The pattern of anomalies at depth resembles the system of salients and embayments that is present offshore western Australia, which formed during rifting of east Gondwana. Previously identified changes in geochemistry of volcanics from Pb isotope anomalies from the inner arc islands correlate with newly identified velocity structures representing the underthrusted and subducted Indo-Australian plate. Reconstruction of uplift from river profiles from the outer arc islands suggests rapid uplift at the ends of the islands of Timor and western Sumba, which coincide with the edges of the volcanic-margin protrusions as inferred from the tomography. These findings suggest that the tectonic evolution of this region is defined by inherited structure of the Gondwana rifted continental margin of the incoming plate. Therefore, the initial template of plate structure controls orogenesis.