Ecological interactions help determine the distribution of species across landscapes and play crucial roles in ecosystem services such as pollination, seed dispersal, and pest control1. Human disturbances, particularly habitat alteration, have the potential to modify or erase ecological interactions2,3 and so jeopardise the processes they control. While examples of interactions becoming rewired under human influence have been recorded, studies of this process for speciose assemblages at regional to continental scales are uncommon4 and obstructed by logistical difficulties2. The consequences for ecological communities and people are therefore poorly understood. Here we show that human habitat alteration is associated with a decrease in the spatial aggregation of Neotropical bat pairs and bird pairs that share similar dietary requirements. We find that groups of species pairs with similar vs. different diets have positive spatial associations on average, but pairs within dietary guilds have stronger associations than pairs with disparate diets when habitats are relatively intact. Our results suggest that species with similar resource requirements typically coexist in relatively intact natural settings. By contrast, exclusion becomes more common (though not dominant) when habitats are altered. Altered habitats thus fail to support the coexistence of diverse competitive interactions, reversing patterns observed in the wild.