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The rapid expansion of human altered landscapes affects biodiversity on every continent. A fundamental goal of conservation biologists is to understand why certain species are at risk of extinction while others are able to persist in human altered landscapes. Afforestation, the conversion of unforested lands to planted forest, is rapidly altering many natural landscapes worldwide. In the Cerrado (Brazilian savanna), a global biodiversity hotspot, a shortage of government incentives has the landscape riddled with abandoned plantation forests that are not subject to active restoration projects. Studies investigating the impacts of abandoned plantations on biodiversity are strikingly limited. We examine the effects of abandoned Eucalyptus plantations on the structure of Cerrado lizard communities. We assessed changes in lizard capture, richness and equitability along cerrado sensu stricto—Eucalyptus transects. Our results indicate abandoned Eucalyptus plantations have subsets of Cerrado species persisting with a great loss of endemic species. The cerrado sensu stricto—Eucalyptus linear transect analysis demonstrated distance from native habitat is positively correlated with loss of biodiversity. We performed correspondence analyses to summarize the variation in species captures across different sites, habitats and pitfall array positions. These analyses depicted strong species associations between habitats and their pitfall array positions. This study is the first to show the negative impacts of abandoned Eucalyptus plantations on Cerrado lizard communities, serving as a cautionary tale of Cerrado biodiversity non-resilience in abandoned Eucalyptus plantations. Mitigation requires that abandoned Eucalyptus plantations are made more suitable to Cerrado lizards by implementing targeted habitat heterogeneity restoration.