Using the threatened greater glider, we integrated biophysical, distribution, and population modelling approaches to account for the interactions between climate change and parallel threats. Our framework combined the effects of wildfire, logging, and habitat fragmentation on populations, while accounting for physiological responses to climate change. Our results suggest additional population declines that would not be captured in other methods. These methods are not specific to a particular species or location and may be used to identify appropriate management actions to conserve threatened species populations around the world.