Climate change and habitat loss are both key threatening processes driving the global loss in biodiversity. Yet little is known about their synergistic effects on biological populations due to the complexity underlying both processes. If the combined effects of habitat loss and climate change are greater than the effects of each threat individually, current conservation management strategies may be inefficient and at worst ineffective. Therefore, there is a pressing need to identify whether interacting effects between climate change and habitat loss exist and, if so, quantify the magnitude of their impact. In this article, we present a meta-analysis of studies that quantify the effect of habitat loss on biological populations and examine whether the magnitude of these effects depends on current climatic conditions and historical rates of climate change. We examined 1319 papers on habitat loss and fragmentation, identified from the past 20 years, representing a range of taxa, landscapes, land-uses, geographic locations and climatic conditions. We find that current climate and climate change are important factors determining the negative effects of habitat loss on species density and/or diversity. The most important determinant of habitat loss and fragmentation effects, averaged across species and geographic regions, was current maximum temperature, with mean precipitation change over the last 100 years of secondary importance. Habitat loss and fragmentation effects were greatest in areas with high maximum temperatures. Conversely, they were lowest in areas where average rainfall has increased over time. To our knowledge, this is the first study to conduct a global terrestrial analysis of existing data to quantify and test for interacting effects between current climate, climatic change and habitat loss on biological populations. Understanding the synergistic effects between climate change and other threatening processes has critical implications for our ability to support and incorporate climate change adaptation measures into policy development and management response.