Landscape conversion by humans may have detrimental effects on animal populations inhabiting managed ecosystems, but human-altered areas may also provide suitable environments for tolerant species. We investigated the spatial ecology of a highly mobile nocturnal avian species–the red-necked nightjar (Caprimulgus ruficollis)–in two contrastingly managed areas in Southwestern Spain to provide management recommendations for species having multiple habitat requirements. Based on habitat use by radiotagged nightjars, we created maps of functional heterogeneity in both areas so that the movements of breeding individuals could be modeled using least-cost path analyses. In both the natural and the managed area, nightjars used remnants of native shrublands as nesting sites, while pinewood patches (either newly planted or natural mature) and roads were selected as roosting and foraging habitats, respectively. Although the fraction of functional habitat was held relatively constant (60.9% vs. 74.1% in the natural and the managed area, respectively), landscape configuration changed noticeably. As a result, least-cost routes (summed linear distances) from nest locations to the nearest roost and foraging sites were three times larger in the natural than in the managed area (mean ± SE: 1356±76 m vs. 439±32 m). It seems likely that the increased proximity of functional habitats in the managed area relative to the natural one is underlying the significantly higher abundances of nightjars observed therein, where breeders should travel shorter distances to link together essential resources, thus likely reducing their energy expenditure and mortality risks. Our results suggest that landscape configuration, but not habitat availability, is responsible for the observed differences between the natural and the managed area in the abundance and movements of breeding nightjars, although no effect on body condition was detected. Agricultural landscapes could be moderately managed to preserve small native remnants and to favor the juxtaposition of functional habitats to benefit those farm species relying on patchy resources.