Understanding how land-use change affects biodiversity is a fundamental step to develop effective conservation strategies in human-modified tropical landscapes. Here, we analyzed how land-use change through tropical small-scale agriculture affects endemic, exotic, and non-endemic native ant communities, focusing on vanilla landscapes in north-eastern Madagascar, a global biodiversity hotspot. First, we compared ant species richness and species composition across seven land-use types: old-growth forest, forest fragment, forest-derived vanilla agroforest, fallow-derived vanilla agroforest, woody fallow, herbaceous fallow, and rice paddy. Second, we assessed how environmental factors drive ant species richness in the agricultural matrix to identify management options that promote endemic and non-endemic native while controlling exotic ant species. We found that old-growth forest, forest fragment, and forest-derived vanilla agroforest supported the highest endemic ant species richness. Exotic ant species richness, by contrast, was lowest in old-growth forest but highest in herbaceous fallows, woody fallows, and rice paddy. Rice paddy had the lowest non-endemic native ant species richness. Ant species composition differed among land-use types, highlighting the uniqueness of old-growth forest in harboring endemic ant species which are more sensitive to disturbance. In the agricultural matrix, higher canopy closure and landscape forest cover were associated with an increase of endemic ant species richness but a decrease of exotic ant species richness. We conclude that preserving remnant forest fragments and promoting vanilla agroforests with a greater canopy closure in the agricultural matrix are important management strategies to complement the role of old-growth forests for endemic ant conservation in north-eastern Madagascar.