Pterosaurs, the first vertebrates to evolve active flight, lived between 210 and 66 million years ago. They were important components of Mesozoic ecosystems, and reconstructing pterosaur diets is vital for understanding their origins, their roles within Mesozoic food webs and the impact of other flying vertebrates (i.e. birds) on their evolution. However, pterosaur dietary hypotheses are poorly constrained as most rely on morphological-functional analogies. Here we constrain the diets of 17 pterosaur genera by applying dental microwear texture analysis to the three-dimensional sub-micrometre scale tooth textures that formed during food consumption. We reveal broad patterns of dietary diversity (e.g. Dimorphodon as a vertebrate consumer; Austriadactylus as a consumer of 'hard' invertebrates) and direct evidence of sympatric niche partitioning (Rhamphorhynchus as a piscivore; Pterodactylus as a generalist invertebrate consumer). We propose that the ancestral pterosaur diet was dominated by invertebrates and later pterosaurs evolved into piscivores and carnivores, shifts that might reflect ecological displacements due to pterosaur-bird competition.