The success of habitat enhancements is typically assessed by subsequent monitoring of the focal taxonomic group. However, enhancement actions are likely to affect other, non-targeted species. On a south-facing slope in the Swiss Jura mountains, a mixed-forest stand was thinned out by irregular removal cuttings to improve the habitat conditions for reptiles. We used this enhancement action as a case study to monitor changes in the macrofungal community that came along with it. During 3 years before and after forest thinning, the site was visited between six and twelve times per year. Thereby, all apparent fungal species were recorded along a ringlike transect, split into 32 transect sections. We used site-occupancy models to estimate fungal species richness and abundance. These models allow to separately estimate occurrence probability and detection probability of species, and to account for differences in detection probability, depending on habitat and season. After the forest thinning, the occurrence probabilities of ectomycorrhizal and saprobic fungi were significantly higher than before. As a result, we estimated a mean increase in overall species richness by 4.4% (median 4.3%, CI 2.1–6.8%) and an increase in abundance by 20.0% (median 19.9%, CI 14.8–25.7%). The two major habitat changes associated with forest thinning, the decrease in living wood and the increase in dead wood on most transect sections, could not explain the whole extent of the estimated increase in species richness and abundance. We believe that forest thinning may have fostered fungal species richness by creating a larger density and diversity of suitable microhabitats. With some caution, we conclude that the small-scale habitat enhancement for reptiles at the Bolberg, creating islands of open forest, did not negatively affect species richness and abundance of macrofungi, a non-targeted species group.