Data underpinning the Current Biology publication "Habitat modification destabilizes spatial associations and persistence of Neotropical carnivores" (doi.org/10.1016/j.cub.2023.07.064). Species detection data for 11 Neotropical carnivores obtained using camera trap methods across a gradient of human habitat modification. Cameras were deployed across 468 sampling locations distributed across nine study landscapes in Colombia. Site-level covariates detailing forest extent, habitat quality and proximity to key environmental resources are also provided. These data were implemented to assess spatial associations between sympatric carnivores across gradients of human habitat modification.