Species loss by habitat replacement operating as an ecological filter is a well‐known consequence of modern human activities. In contrast, the ecological and evolutionary response of species overcoming those filters in converted habitats has not been thoroughly explored. Species that persist are subject to novel and potentially stressful conditions that may induce certain morphological changes. We evaluated changes in the functional morphology of three anuran species persisting after the conversion of areas of the Atlantic Forest into pine plantations. We specifically evaluated differences in body size and body condition indices, head width, and hind legs’ length between adult individuals from both habitats and sexes. Habitat conversion and sexual dimorphism affected the morphology of the three anurans, with varying effects upon species and traits. Regarding the effect of habitat conversion, Elachistocleis bicolor increased body condition in plantations with no changes in the other traits, Physalaemus cuvieri showed only a marginal increment in residual body mass in plantations, and Odontophrynus americanus exhibited a substantial increment in body size while maintaining its body condition in plantations. Remarkably, none of the results suggested these persistent anurans were stressed by forest conversion. This study shows that habitat conversion may induce intraspecific morphological changes in ecologically relevant traits of persistent species, and that disturbed areas do not necessarily imply stressful, low quality habitats affecting all persistent native species negatively.