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Drylands worldwide are experiencing shrub encroachment into grasslands with potential consequences for biodiversity and ecosystem services. Climate change could increase the rate of shrub encroachment, amplify precipitation variability, and thus alter bottom-up processes for animal communities. Desert rodents are important biodiversity elements of arid grasslands and shrublands that exert strong effects on soil, vegetation, and other animal species. We used long-term data from the Jornada Basin Long Term Ecological Research site in the Chihuahuan Desert of southern New Mexico to ask whether bottom-up control of desert rodents changes across shrub encroachment gradients. Our design included spatial blocks with replicated ecological states representing transitions from black grama (Bouteloua eriopoda) to honey mesquite (Prosopis glandulosa). Grassland-to-shrubland transitions did not produce degraded ecosystems, on average, with reduced net primary production or decreased rodent biomass. However, more rodent biomass was supported on unencroached grasslands following droughts whose frequency and severity may increase in southwestern United States. Hence, the observed evenness in rodent biomass across ecological states should be sensitive to climate change. The best predictors of rodent biomass also differed markedly for two trophic groups. This outcome was explained by considering core-transient dynamics. Granivores were mostly core species that regularly occurred on sites and responded to lagged net primary production at local scales, whereas folivores included transient species (especially Sigmodon hispidus) that responded to lagged precipitation at broader scales via spillover dynamics. Bottom-up processes for desert rodents across shrub invasion gradients were understood by integrating lagged responses to productivity pulses with core-transient structuring of communities.