Abstract Background and aims Inland sand dunes constitute Natura 2000 habitat that has become a priority to ensure biodiversity protection and habitat heterogeneity at the landscape scale; however, without proper management, spontaneous succession leads to overgrowing of trees and thus to habitat degradation. Understanding succession processes, relationships between biotic and abiotic components, and their changes over time after restoration, is the key to proper planning of future restoration activities. The aim was to determine the changes of biological soil crust (BSC), vascular plants and physicochemical parameters of BSC, below-crust, rhizosphere, and bare substrate types at different stages of succession in inland dunes of the Błędowska Desert (Poland). We also analyzed the interplay between these factors to further understand the mechanism of BSC development and recognize driving factors causing changes in the soil environment. Results Our results showed that BSCs contributed to increased organic C, total N, nutrients in soil, and acidification with the succession. The content of inorganic N forms was significantly higher in bare soil compared to below-crust soil. Rhizosphere soil was enriched in organic matter and nutrients, which improves soil conditions within plant patches. Moreover, below-crust soil pH, total N content and water holding capacity drive the patterns of BSC morphological groups and species composition of lichens, bryophytes, and vascular plants. Conclusion Our study shows that spatial structure of the inland dune ecosystem is a mosaic of BSCs and plants that contribute to the spatial heterogeneity of key soil properties. We concluded that it is necessary to consider the matter of BSC in restoration treatments.