The soil seed bank is crucial for the stability and regeneration of the specialised gypsum plant communities. The presence of shrubs influences the spatial structure of the soil seed bank by trapping more or fewer seeds depending on their physiognomic attributes or, for example, by providing seeds through the plants established under canopies. We aimed to unravel the potential role of different shrub species with diverse physiognomy in determining the spatial structure of the soil seed bank in a semi-arid gypsum plant community of NE Spain. We examined richness and abundance of the soil seed bank at different microsites associated with four dominant shrubs of different size-type (tall or short), and architecture (crawling-branched or erect). We found more considerable richness and abundance of seeds of perennial species within shrub canopies than in open areas. Specifically, the crawling-branched shrubs Gypsophila struthium and Helianthemum squamatum, and the tall erect shrub Ononis tridentata accumulated the most abundant soil seed banks of perennials, thus having an important structuring role. Conservation and restoration efforts should focus on gypsophyte shrubs (G. struthium, O. tridentata and H. squamatum), which can enhance community stability and regeneration through the formation of an abundant soil seed bank of perennial species in gypsum plant communities.