Agricultural modification is one of the main drivers of global biodiversity decline. Vegetation clearance, tillage, grazing, and the application of fertilisers and pesticides have significantly affected native plants and animals. Reptiles can be vulnerable to agricultural practices, and localised declines in reptile biodiversity have been detected. However, the causes of these declines are likely to be many and will vary among reptiles with different life histories. Fossorial reptiles (those that mainly live below ground) are likely to be particularly vulnerable to soil and ground cover disturbance and yet are little studied in the context of agricultural practices. Here, we test the proposition that habitat disturbance caused by agricultural modification is a good predictor of decline or absence of a fossorial lizard. Specifically, we used boosted regression trees to model the relationship between five habitat factors and site abundance of the threatened Pink-tailed Worm-lizard (Aprasia parapulchella; Pygopodidae). We found that vegetation characteristics were the best predictors of A. parapulchella abundance. In particular, the relative contributions to our model of percentage cover of native large tussock-forming grasses and site floristic score were 46% and 33%, respectively. Other variables that contributed to the explanation of abundance were percentage cover of rocks (10%), number of turnable rocks (5%) and relative density of rocks occupied by ants of the size class known to occur with A. parapulchella (5%). Our findings suggest that agricultural management or restoration strategies that promote ground-layer vegetation characteristic of low levels of modification are likely to be most beneficial for the conservation of this species. Our findings and methods may be applicable to understand and study the presence and abundance of other fossorial or semi-fossorial reptiles with specialised habitat preferences. Further research is required to establish the generality of our findings with respect to other such species around the world.