The study of species coexistence and community assembly has been a hot topic in ecology for decades. Disentangling the hierarchical role of abiotic and biotic filters is crucial to understand community assembly processes. The most critical environmental factor in semi-arid environments is known to be water availability, and perennials are usually described as nurses that create milder local conditions and expand the niche range of several species. We aimed to broaden this view by jointly evaluating how biological soil crusts (BSCs), water availability, perennial species (presence/absence of Stipa tenacissima) and plant-plant interactions shape a semi-arid annual plant community. The presence and cover of annual species was monitored during three years of contrasting climate. Water stress acted as the primary filter determining the species pool available for plant community assembly. Stipa and BSCs acted as secondary filters by modulating the effects of water availability. At extremely harsh environmental conditions, Stipa exerted a negative effect on the annual plant community, while at more benign conditions it increased annual community richness. Biological soil crusts exerted a contradictory effect depending on climate and on the presence of Stipa, favoring annuals in the most adverse conditions but showing repulsion at higher water availability conditions. Finally, interactions among co-occurring annuals shaped species richness and diversity of the final annual plant assembly. This study sheds light on the processes determining the assembly of annual communities and highlights the importance of Biological Soil Crusts and of interactions among annual plants on the final outcome of the species assembly.