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The effects of habitat fragmentation on plant–animal interactions may emerge at different spatial scales, depending on the species-specific perception response of the interacting animals. Furthermore, changes in habitat cover and configuration commonly occur simultaneously, hampering efforts to understand and mitigate the impact of fragmentation on these biotic interactions. In order to account for the relative influence of habitat loss and fragmentation on plant–animal interactions, we quantified habitat structure in sixteen sectors (nested circular areas of 100 and 200 m radii) in four different localities (four sectors per locality) across the Cantabrian Range in NW Spain. In the center of each 100 m radius sector, we measured the magnitude of two ecologically opposite (mutualistic vs antagonistic) interactions in individual holly trees Ilex aquifolium which strongly determine the regeneration process in this plant species: frugivory by birds and seed predation by rodents. We found that habitat fragmentation, though not habitat loss, affected the magnitude of both plant–animal interactions. However, these effects were conditioned by the strong differences in spatial heterogeneity in habitat structure between localities. In fact, the effect of habitat fragmentation on both plant–animal interactions disappeared when the locality in which sectors were sited was taken into account. This study highlights that 1) habitat spatial configuration, far from being a negligible component of habitat structure, is in fact able to influence key ecological processes such as plant–animal interactions, and 2) the potential spatial and structural complexity of localities makes a regional approach (i.e. that involving many localities) indispensable in the quest for comprehensive understanding of the effects of habitat structure on biodiversity in real-world fragmented landscapes.