Amphisbaenians are reptiles specialized for a fossorial lifestyle, which may limit their opportunities for microhabitat selection in comparison with epigeal reptiles. We hypothesized that, given the fossorial habits of amphisbaenians, a detailed analysis of the physical and chemical properties of the soil may reveal their patterns of habitat use. We investigated microhabitat and soil use by a population of the amphisbaenian Trogonophis wiegmanni from the Chafarinas Islands (North-West Africa) and compared them with those available in the habitat. Results showed that some soil physical and chemical characteristics determined microhabitat use by T. wiegmanni. Amphisbaenians selected soils that were relatively sandy, basic, carbonated and shallow, having a high cover of medium-sized rocks, whereas they avoided marine salinized, more acid and deeper heavy-textured soils (i.e. with percentages of silt comparatively high), and those covered mainly by small rocks. No differences were found between soils with and without influence of seabird colonies, although this was the main driver of soil chemical variations in these Islands. Vegetation cover per se did not seem to have a direct influence on microhabitat use. We discuss how energetic costs of burrowing and the direct and indirect influences of soil chemical properties could explain these patterns of habitat use.