The presence of exotic predators in ecosystems across the world is a leading driver of native species’ declines. Exotic predators largely influence native species through predation and harassment, which may cause native species to avoid them spatially. We used a camera trap dataset from seven sites in Madagascar's largest protected area complex to investigate spatial co‐occurrence patterns between three exotic predators (free‐ranging domestic dogs Canis familiaris and cats Felis silvestris, and small Indian civet Viverricula indica) and native ground‐dwelling forest birds (n = 5) and small mammals (n = 4). We created 216 two‐species occupancy models for 27 exotic predator‐native species pairings to examine how habitat, exotic predator presence or both, influenced each native species’ occupancy and/or detection. We found that native bird and small mammal occupancy and/or detection were strongly related to an exotic predator's presence 52% of the time (i.e. 14 of 27 exotic predator‐native species pairings). Six of the 14 species pairings (i.e. 43%) had non‐independent co‐occurrence patterns, four of which were habitat‐mediated. The effect of exotic predator presence on native species’ detection was largely negative, depressing native species’ detection in seven out of 12 instances (i.e. 58% of the time). The small Indian civet and free‐ranging cats each strongly influenced the occupancy and/or detection of six species for a combined impact on seven native species, while domestic dogs strongly influenced two species. By including habitat covariates in two‐species occupancy models, we gained deeper insight into the effect exotic predator presence has on native species’ distribution. We also note that the strong effect of exotic predator presence on our ability to detect native species can hinder the ability of researchers to provide accurate parameter estimates. We recommend future research into the synergistic effects that habitat degradation and exotic species presence has on native species.