Lantana (Lantana camara L., Verbenaceae) is an invasive species of global interest that threatens more than 300 Australian plant and animal species of conservation significance. Reptiles may be at high risk due to their ground-dwelling habit and reliance on microhabitat structure. We examined the effects of lantana, and its management, on reptile assemblages in a wet sclerophyll forest in southeast Queensland, Australia. We compared reptile assemblages across four treatments: (i) manual clearing and herbicide application; (ii) herbicide application followed by prescribed burn; (iii) untreated lantana thickets; and (iv) wet sclerophyll forest. Plots treated with herbicide and then burned were structurally more diverse than manually cleared sites and supported a greater diversity of reptiles. No species occurred exclusively in untreated lantana habitats; however, these plots supported relatively high abundances of rare species, particularly Challenger Skinks (Saproscincus rosei). Lantana also had a higher species richness compared to manually cleared and sclerophyll forest. The use of lantana as habitat by a number of species highlights the need to consider the importance of these habitats for fauna prior to implementing management options. Herbicide application followed by prescribed burning appears to be an ideal approach to manage lantana due to the increased heterogeneity and regrowth of native vegetation, an option which supported more diverse reptile communities. Our results caution against the whole scale clearing of lantana from invaded areas, as these habitats continue to support reptile communities including threatened species. Nevertheless, by treating lantana with herbicide and prescribed fire, reptile community structure might be maintained.