Abstract Morphological integration of skull modules can explain the outstanding morphological diversity of the rostrum in phyllostomids, the largest radiation of bats in the Western Hemisphere. However, the covariation of the rostral and caudal modules within adaptive zones, where specializations may impose constraints on morphological diversification, remains unknown. Here we used phylogenetic linear models and accounted for phylogenetic uncertainty to examine the evolutionary relationship between brain volume—as a proxy for neurocranium size—and palate morphology in 42 species of specialized frugivores of the subfamily Stenodermatinae. We found that the palate surface area increased and became relatively wider as brain size increased. This pattern may be pervasive in frugivorous phyllostomids, although different lineages may show different rates of covariation. These results demonstrate that the tight relationship between the two main modules of the skull is consistent at different macroevolutionary scales, providing new insights into the macroevolutionary dynamics of the largest group of Neotropical frugivorous bats.