The mechanisms supporting positive ecological interactions are important. Foundation species can structure desert biodiversity by facilitating seedbanks of annual plants, but the direct and indirect mechanisms of shrub effects on seedbank have not been experimentally decoupled. We conducted the first test of shrubs increasing seedbank densities through direct effects on the seedbank (i.e. shrub seed-trapping, animal-mediated dispersal) and indirect effects by facilitating the annual plant community (i.e. seed deposition, annual seed-trapping). Two distinct desert ecosystems were used to contrast transient seedbank densities in shrub and open microsites by manipulating annual plant density and the presence of the persistent seedbank. We measured transient seedbank densities at the end of the growing season by collecting soil samples and extracting seeds from each respective treatment. Transient seedbank densities were greatest in shrub canopies and with relatively higher annual plant densities. The persistent seedbank contributed to transient seedbank densities only in one desert and in the open microsite. Shrubs indirectly increased seedbank densities by facilitation the seed production of the annual plants. Therefore, shrubs are increasing seedbank independently of the annual plant community, likely through trapping effects, and dependently by facilitating seed production of the annuals. These findings provide evidence for a previously undescribed mechanism that supports annual seedbanks and thus desert biodiversity. We also identify shrubs as being significant drivers of desert plant communities and emphasize the need to consider multiple mechanisms to improve our ability to predict the response of ecosystems to change.