Increased urbanisation influences the morphometric traits of various species, often resulting in urban individuals being smaller than their non-urban counterparts. Urbanisation can affect fundamental eco-evolutionary patterns and impact species’ ability to adapt to and occupy rapidly changing environments through morphological changes. We investigated the morphometric responses of two passerine species, the non-native house sparrow (Passer domesticus) and its native congener, the Cape sparrow (Passer melanurus), along gradients of spatial and temporal urbanisation in South Africa over a 52-year period. The house sparrow was significantly heavier, larger and in better condition with increasing urban infrastructure and lower urban vegetation cover, while the Cape sparrow showed opposing trends along these gradients. Temporally, the house sparrow’s body mass increased consistently over the 52-year study period, suggesting changes in morphology were concomitant with increasing urbanisation over time. This study demonstrates distinct differences in the morphological responses of the non-native house sparrow and the native Cape sparrow to increasing urban development. These morphological responses may also underpin community-level changes caused by urbanisation, enhancing the capabilities of non-native species to thrive over their native counterparts in these environments.