- Abstract: Anthropogenic habitat perturbation is a major cause of population decline. A standard practice managers use to protect populations is to leave portions of natural habitat intact. We describe a case study in which, despite the use of this practice, the critically endangered lizard Acanthodactylus beershebensis was locally extirpated from both manipulated and natural patches within a mosaic landscape of an afforestation project. We hypothesized that increased structural complexity in planted patches favors avian predator activity and makes these patches less suitable for lizards due to a heightened risk of predation. Spatial rarity of natural perches (e.g., trees) in arid scrublands may hinder the ability of desert lizards to associate perches with low‐quality habitat, turning planted patches into ecological traps for such species. We erected artificial trees in a structurally simple arid habitat (similar to the way trees were planted in the afforestation project) and compared lizard population dynamics in plots with these structures and without. Survival of lizards in the plots with artificial trees was lower than survival in plots without artificial trees. Hatchlings dispersed into plots with artificial trees in a manner that indicated they perceived the quality of these plots as similar to the surrounding, unmanipulated landscape. Our results showed that local anthropogenic changes in habitat structure that seem relatively harmless may have a considerable negative effect beyond the immediate area of the perturbation because the disturbed habitat may become an ecological trap.