The politics of territoriality in Northeast India cannot be adequately understood through conventional binaries of state sovereignty versus ethnic separatism. This article examines the contested territorial formations of Manipur and Nagaland, where competing claims to land, political authority, historical belonging, and collective self-determination intersect with the Indian state’s territorial sovereignty. It argues that the central problem is not merely the incompatibility of ethnic claims but the coexistence of multiple, overlapping territorial imaginaries that seek political recognition through mutually constraining spatial projects. In Manipur, competing Meitei, Naga, Kuki, and state-centred territorial claims reveal how historically differentiated political communities construct incompatible narratives of homeland, indigeneity, security, and territorial entitlement. In Nagaland, the Naga national movement similarly challenges the territorial finality of postcolonial state boundaries, while the institutionalisation of statehood has generated a complex distinction between territorial governance and broader Naga political aspirations. The article develops the concept of “layered contested territoriality” to theorise this condition: territory is neither a fixed container of sovereignty nor an objective geographical space, but a continuously negotiated political field in which state, ethnic, and Indigenous authorities claim overlapping forms of legitimacy. Building on Indigenous political theory and scholarship on sovereignty and territoriality, the article interrogates how state recognition can simultaneously accommodate and constrain competing claims. It further demonstrates that attempts to resolve territorial disputes through administrative reorganisation alone risk reproducing the very exclusions that sustain contestation. By placing Manipur and Nagaland within a comparative framework, the article advances a relational understanding of sovereignty in which territorial peace requires not simply settling boundaries but negotiating among competing jurisdictions, historical memories, and political futures.