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Habitat destruction and overexploitation are the main threats to biodiversity and where they co‐occur, their combined impact is often larger than their individual one. Yet, detailed knowledge of the spatial footprints of these threats is lacking, including where they overlap and how they change over time. These knowledge gaps are real barriers for effective conservation planning. Here, we develop a novel approach to reconstruct the individual and combined footprints of both threats over time. We combine satellite‐based land‐cover change maps, habitat suitability models and hunting pressure models to demonstrate our approach for the community of larger mammals (48 species > 1 kg) across the 1.1 million km² Gran Chaco region, a global deforestation hotspot covering parts of Argentina, Bolivia and Paraguay. This provides three key insights. First, we find that the footprints of habitat destruction and hunting …