Developmental changes through an animal’s life are generally understood to contribute to the resulting adult morphology. A possible exception are species with complex life cycles, where individuals pass through distinct ecological and morphological life stages during their ontogeny, ending with metamorphosis to the adult form. Antagonistic selection is expected to drive low genetic correlations between life stages, theoretically permitting stages to evolve independently. Using the Australian frog radiation, we examine the evolutionary consequences on morphological evolution when life stages are under different selective pressures. We use morphometrics to characterise body shape of tadpoles and adults across 166 species of frog and investigate similarities in the two resulting morphological spaces (morphospaces) to test for concerted evolution across metamorphosis in trait variation during speciation. A clear pattern emerges: Australian frogs and their tadpoles are evolving independently; their drastically different morphospaces and contrasting estimated evolutionary histories of body shape diversification indicate that different processes are driving morphological diversification at each stage. Tadpole morphospace is characterised by rampant homoplasy, convergent evolution and high lineage density; the adult morphospace by contrast shows greater phylogenetic signal, low lineage density and divergent evolution between the main clades. Our results provide insight into the macroevolutionary consequences of a biphasic life cycle.