The Himalayan orogen has experienced intense Cenozoic deformation and widespread metamorphism, making it difficult to track its initial architecture and the subsequent deformation path during the Cenozoic India-Asia collision. To address this issue, we conducted structural mapping and U-Pb zircon geochronology across the Shillong Plateau, Mikir Hills, and Brahmaputra River Valley of northeastern India, located 30–100 km south of the eastern Himalaya. Our work reveals three episodes of igneous activity at ca. 1600 Ma, ca. 1100 Ma, and ca. 500 Ma, and three ductile-deformation events at ca. 1100 Ma, 520–500 Ma, and during the Cretaceous. The first two events were contractional, possibly induced by assembly of Rodinia and Eastern Gondwana, while the last event was extensional, possibly related to breakup of Gondwana. Because of its proximity to the Himalaya, the occurrence of 500 Ma contractional deformation in northeastern India implies that any attempt to determine the magnitude of Cenozoic deformation across the Himalayan orogen using Proterozoic strata as marker beds must first remove the effect of early Paleozoic deformation. The lithostratigraphy of the Shillong Plateau established by this study and its correlation to the Himalayan units imply that the Greater Himalayan Crystalline Complex may be a tectonic mixture of Indian crystalline basement, its Proterozoic-Cambrian cover sequence, and an early Paleozoic arc. Although the Shillong Plateau may be regarded as a rigid block in the Cenozoic, our work demonstrates that distributed active left-slip faulting dominates its interior, consistent with earthquake focal mechanisms and global positioning system velocity fields across the region.