Cranial morphology is remarkably varied in living amniotes, ranging from short-faced mammals to the elongate snouts of crocodylians. This diversity of shapes is thought to correspond with feeding ecology, a relationship repeatedly demonstrated at smaller phylogenetic scales, but one that remains untested across amniote phylogeny. Using a combination of 2D geometric and linear morphometrics, we investigate the links between phylogenetic relationships, diet, and skull shape in an expansive dataset of extant amniotes with teeth: mammals, lepidosaurs, and crocodylians. We find that both phylogeny and diet have statistically significant effects on skull shape, although these effects differ depending on the dataset analyzed. The three major clades largely partition morphospace, each plotting in separate regions with limited overlap. Mammals and squamates extensively diversify within their respective regions. Among all three groups, dietary generalists often occupy clade-specific central regions of morphospace. Some parallel changes in skull shape occur in clades with distinct evolutionary histories but similar diets. However, members of a given clade often present distinct skull shape solutions for a given diet, and the vast majority of species retain the unique aspects of their ancestral skull plan, underscoring the limits of morphological convergence due to ecology in amniotes. These data demonstrate that certain skull shapes may provide functional advantages suited to particular diets, but accounting for both phylogenetic history and ecology can provide a more nuanced approach for inferring the ecology and functional morphology of cryptic or extinct amniotes.