Habitat fragmentation may present a major impediment to species range shifts caused by climate change, but how it affects local community dynamics in a changing climate has so far not been adequately investigated empirically. Using long-term monitoring data of butterfly assemblages, we tested the effects of the amount and distribution of semi-natural habitat (SNH), moderated by species traits, on climate-driven species turnover. We found that spatially dispersed SNH favoured the colonisation of warm-adapted and mobile species. In contrast, extinction risk of cold-adapted species increased in dispersed (as opposed to aggregated) habitats and when the amount of SNH was low. Strengthening habitat networks by maintaining or creating stepping-stone patches could thus allow warm-adapted species to expand their range, while increasing the area of natural habitat and its spatial cohesion may be important to aid the local persistence of species threatened by a warming climate.