This article examines centre–periphery relations in post-colonial India and Pakistan, providing a specific comparative history of autonomy movements in Nagaland (1947–63) and Baluchistan (1973–7). It highlights the key role played by the central government – particularly by Jawaharlal Nehru and Zulfikar Ali Bhutto – in quelling both insurgencies and in taking further steps to integrate these regions. It argues that a shared colonial history of political autonomy shaped local actors’ resistance to integration into the independent nation-states of India and Pakistan. This article also reveals that Indian and Pakistani officials used their shared colonial past in very different ways to mould their borderlands policies. India's central government under Nehru agreed to a modified Naga State within the Indian Union that allowed the Nagas a large degree of autonomy, continuing a colonial method of semi-integration. In contrast, Bhutto's government actively sought to abandon long-standing Baluch political and social structures to reaffirm the sovereignty of the Pakistani state. The article explains this divergence in terms of the different governing exigencies facing each country at the time of the insurgencies. It ultimately calls for an expansion in local histories and subnational comparisons to extend understanding of post 1947 South Asia, and the decolonizing world more broadly.