Despite severe population declines and an overall range contraction, some populations of large carnivores have managed to survive in human‐modified landscapes. From a conservation perspective, it is important to identify the factors allowing for this coexistence, including the relevant habitat characteristics associated with the presence of large carnivores. We evaluated the role of several environmental factors describing habitat quality for wolves Canis lupus in the humanised Iberian Peninsula, which currently holds an important wolf population at European level. We used maximum entropy and generalized linear model approaches in a nested‐scale design to identify the environmental factors that are related to wolf presence at three spatial scales and resolutions: (1) distribution range: wolf presence on a 10 × 10 km grid resolution, (2) wolf habitat use: wolf occurrence on a 2 × 2 km grid and (3) dens/rendezvous sites: breeding locations on a 1 × 1 km grid. Refuge availability, as defined by topography, seemed to be the key factor determining wolf presence at the multiple scales analysed. As a result, wolf populations may coexist with humans in modified landscapes when the topography is complex. We found that a significant amount of favourable habitat is not currently occupied, suggesting that the availability of suitable habitat is not the limiting factor for wolves in the Iberian Peninsula. Habitat suitability outside the current range indicates that other factors, such as direct persecution and other sources of anthropogenic mortality, may be hampering its expansion. We suggest that priorities for conservation should follow two general lines: (1) protect good quality habitat within the current range; and (2) allow dispersal to unoccupied areas of good quality habitat by reducing human‐induced mortality rates. Finally, we still need to improve our understanding of how wolves coexist with humans in modified landscapes at fine spatiotemporal scales, including its relationship with infrastructures, land uses and direct human presence. Wolf populations may coexist with humans in modified landscapes when the topography is complex. A significant amount of favourable habitat is not currently occupied. Habitat suitability outside the current range indicates that other factors, such as direct persecution and other sources of anthropogenic mortality, may be hampering its expansion. Photo Credit : Joaquim Pedro Ferreira