A legacy of theories of culture change and assimilation is the assumption that the more intrusive the imperial social engineering policies, the more Indigenous cultures change. Instead, we argue that Indigenous cultural persistence can flourish despite imperial consolidation. We describe two ways that Indigenous identities are reinforced under imperial state consolidation. The first is top-down, where the empire codifies diverse identities that were fluid and not legible to the state. The second is bottom-up, where local Indigenous cultures pushed back against the rigid and divisive state-sponsored identity categories. We argue that because the bottom-up persistence of Indigenous identities is creative and fluid, material culture can change rapidly. We argue that this kind of persistence, not predicated on superficial material continuities but on core beliefs and praxis, deserves attention and analysis. We show how in the Andes, local Indigenous cultures were able to overcome top-down social engineering and persist in robust, creative ways. This creativity led to an Indigenous-led cosmopolitanism that spread Indigenous culture even to mestizos and poor Spaniards, as in the case of the formation of Morochuco identity in highland Peru. These new cosmopolitan identities based on traditional Indigenous lifeways would ultimately prove pivotal in winning independence for South America.