Forest fragmentation reduces the amount of forest cover and negatively affects the habitat quality of forest remnants. Landscape attributes and habitat quality should therefore be evaluated together to improve our understanding of how fauna respond to fragmentation. We evaluated how patch quality (vegetation structure) and landscape characteristics influence the abundance of phytophagous bats in two contrasting types of landscape that differ in percent forest cover and matrix type: landscapes dominated by man-made pastures and landscapes with large tracts of continuous forest (tropical semi-deciduous forest). Bats were sampled in forest patches in both types of matrices, and for each matrix two sites with a cenote (water filled sink-holes, typical of the Yucatan) and two with no cenotes were sampled. Sites with cenotes offer better habitat quality than sites without cenotes: the richness and basal area of plants eaten (flower or fruit) by bats are higher in the forest vegetation surrounding them. At the landscape level, phytophagous bat abundance was negatively correlated with the amount of forest cover and proximity to other forest fragments, but positively correlated with forest edge density, patch density and landscape heterogeneity. At the patch level, bat abundance was positively correlated with plant richness and the basal area of edible tree species. In the Yucatan's agricultural landscapes the area and spatial distribution of forest remnants are not the only variables affecting bats. Habitat patch quality and high heterogeneity of land cover types are also important, and have a positive effect on phytophagous bat abundance and movement.