Indigenous organizations in the Andean countries of Ecuador and Bolivia originated novel proposals to pluralize sovereign arrangements through plurinational statehood. Reflecting diverse Indigenous groups’ relations with postcolonial states, these proposals created a unique basis for re-negotiating (sovereign) resource governance. Despite the constitutional endorsement of the plurinational state model however, the latest empirical evidence confirms growing state control over subsoil resources that excises Indigenous peoples from decision-making over resources. In this paper, we trace the emergence of novel agendas for sovereignty-multiplicity, showing how Indigenous agendas had anticipated the need to go beyond their rights over subsoil resources and autonomous territories. These agendas implied re-negotiating national sovereignty in light of the countries’ internal ethno-political and epistemic heterogeneity. Under nominally plurinational states however, resource governance outcomes perpetuate and normalise longstanding epistemic and power differentials between rights-bearing political subjects and Indigenous subjects. We highlight the colonial-modern bases of current sovereignty arrangements, identifying the presumptions and legal parameters that shape the dynamics between states, people and Indigenous people. Situating resource governance in relation to the concept of modernity/coloniality, we propose to (re)think sovereignty arrangements in the colonial present in light of internal heterogeneity.