The effects of biological soil crusts (BSC) on vascular plant growth can be positive, neutral or negative, and little information is available on the impacts of different BSC successional stages on vascular plant population dynamics.• We analysed seedling emergence, survival, plant growth and reproduction in response to different BSC successional stages (i.e. habitats: bare soil, cyanobacteria, lichen and moss crusts) in natural populations of Echinops gmelinii Turcz. in the Tengger Desert of northwest China. The winter annual E. gmelinii is a dominant pioneer herb after sand stabilisation.• During the early stages of BSC succession, the studied populations of E. gmelinii were characterised by high density, plant growth and fecundity. As the BSC succession proceeded beyond moss crusts, the fecundity decreased sharply, which limited seedling recruitment. Differences in seedling survival among the successional stages were not evident, indicating that BSC have little effect on survival in arid desert regions. Moreover, E. gmelinii biomass allocation exhibited low plasticity, and only reproductive allocation was sensitive to the various habitats. Our results further suggest that the negative effects of BSC succession on population dynamics are primarily driven by increasing topsoil water-holding capacity and decreasing rain water infiltration into deeper soil.• We conclude that BSC succession drives population dynamics of E. gmelinii, primarily via its effect on soil moisture. The primary cause for E. gmelinii population decline during the moss-dominated stage of BSC succession is decreased fecundity of individual plants, with declining seed mass possibly reducing the success of seedling establishment.