Understanding how habitat loss and overhunting impact large carnivores is important for broad-scale conservation planning. We aimed to assess how these threats interacted to affect jaguar habitat (Panthera onca) between 1985–2013 in the Gran Chaco, a deforestation hotspot. Location: Gran Chaco ecoregion in Argentina, Paraguay and Bolivia. We modelled jaguar habitat change from 1985–2013 using a time-calibrated species distribution model that uses all occurrence data available for that period. We modelled habitat as a function of resource availability and hunting threats, which allowed us to separate core (high resource availability and low hunting threat), refuge (low resources but safe), attractive sink (high resources but risky) and sink (low resources and risky) habitat for 1985, 2000 and 2013. Jaguar core areas contracted by 33% (82,400 km2) from 1985–2013, mainly due to an expansion of hunting threats. Sink and attractive sink habitat covered 58% of the jaguar range in 2013 and most confirmed jaguar kill sites occurred in these areas. Furthermore, habitat loss and hunting threats co-occurred in 29% of jaguars’ range in 2013. Hunting threats also deteriorated core areas within protected areas, but 95% of all core areas loss occurred outside protected lands. About 68% of the remaining core areas in 2013 remained unprotected, mostly close to international borders. Our study highlights the synergistic effects that habitat loss and hunting threats exert on large carnivores, even inside protected areas, emphasizing the need to consider the geography of threats in conservation planning. Our results also point to the importance of areas along international borders as havens for wildlife and thus the urgent need for cross-border planning to prevent the imminent extinction of jaguars from the Chaco. Opportunities lie in reducing jaguar mortality over the widespread attractive sinks, particularly in corridors connecting core areas.