The inner ear labyrinth is an organ able to perceive balance and spatial orientation, but the drivers of its morphological variation across and within vertebrate lineages are unclear. We assess two competing hypotheses whether this organ, and specifically the semicircular canals, modifies its shape as a functional adaptation to ecology and locomotion, or according to the constraints of skull morphology. We test these using 52 species of Australian sphenomorphines, a group of scincid lizards that evolved changes in body shape and locomotory adaptations to fossoriality multiple times independently, by reducing their limbs. We find a correlation between semicircular canal shape and degree of limb reduction in these lizards, supporting a functional hypothesis. The interaction between body shape and substrate ecology is also a significant predictor. The wider and more eccentric semicircular canals of limb-reduced skinks indicate higher balance sensitivity and manoeuvrability compared with fully limbed skinks, probably as an adaptation to navigating cluttered environments. Conversely, our results show only a minimal influence of skull constraints on semicircular canal shape, having instead significant effects on size. This supports the hypothesis that in these skinks inner ear shape evolution is driven by specific locomotory strategies more than it is constrained by cranial anatomy.