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We report on the effects of almost a decade of 1080-fox baiting on a lizard community in a mosaic Australian habitat. Replicated comparisons of baited versus non-baited control areas with near-identical histories of bush fires, grazing and climate showed a higher density of red fox tracks (Canis vulpes) in the non-baited areas. Furthermore, the fox-baited areas showed a more than five times higher density of sand goannas (Varanus gouldii), a species that strongly overlaps the red fox in food niche breadth and is itself a direct target of fox predation, in particular its eggs and young. Exclusion of predators from a natural habitat led to significant increases in the density of small lizards, suggesting that predation can drive lizard population dynamics in this ecosystem. Replicated pitfall-trapping in three habitats in the control areas (with high fox and low goanna density) versus the baited areas (with low fox and high goanna density) showed that fox baiting had positive effects on the density of diurnal scincid lizards in open grassland, whereas the control areas showed higher density of nocturnal gecko lizards. Our interpretation is that fox removal may result in a shift in the top predator towards the sand goanna. Historically, this indigenous, endemic species was the natural top predator. It has co-evolved with its prey and that may have moulded it into a more efficient lizard predator per encounter than the introduced fox.