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Land‐cover change and ecosystem degradation may lead to biotic homogenization, yet our understanding of this phenomenon over large spatial scales and different biotic groups remains weak. We used a multi‐taxa dataset from 335 sites and 36 heterogeneous landscapes in the Brazilian Amazon to examine the potential for landscape‐scale processes to modulate the cumulative effects of local disturbances. Biotic homogenization was high in production areas but much less in disturbed and regenerating forests, where high levels of among‐site and among‐landscape β‐diversity appeared to attenuate species loss at larger scales. We found consistently high levels of β‐diversity among landscapes for all land cover classes, providing support for landscape‐scale divergence in species composition. Our findings support concerns that β‐diversity has been underestimated as a driver of biodiversity change and underscore the importance of maintaining a distributed network of reserves, including remaining areas of undisturbed primary forest, but also disturbed and regenerating forests, to conserve regional biota.