Abstract Allometry, i.e., morphological variation correlated with size, is a major pattern in organismal evolution. Since size varies both within and among species, allometry occurs at different variational levels. However, the variability of allometric patterns across levels is poorly known since its evaluation requires extensive comparative studies. Here, we implemented a 3D geometric morphometric approach to investigate cranial allometry at three main variational levels—static, ontogenetic, and evolutionary—and two anatomical scales—entire cranium and cranial subunits—based on a dense intra- and interspecific sampling of extant armadillo diversity. While allometric trajectories differ among distantly related species, they hardly do so among sister families. This suggests that phylogenetic distance plays an important role in explaining allometric divergences. Beyond trajectories, our analyses revealed pervasive allometric shape changes shared across variational levels and anatomical scales. At the entire cranial scale, craniofacial allometry (relative snout elongation and braincase reduction) is accompanied notably by variations of nuchal crests and postorbital constriction. Among cranial subunits, the distribution of allometry was highly heterogeneous, with the frontal and petrosal bones showing the most pervasive shape changes, some of which were undetected at a more global scale. Evidence of widespread and superimposed allometric variations raises questions on their determinants and anatomical correlates and demonstrates the critical role of allometry in morphological evolution.