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Exotic invasive plant species alter ecosystems and locally extirpate native plant species, and by doing so alter community structure. Changes in community structure may be particularly important if invaders promote species with certain traits. For example, the positive effects of most invaders on soil fertility may promote species with weedy traits, whether native or not. We examined the effects of two co-occurring Prosopis congeners, the native P. cineraria and the exotic invader P. juliflora, on species identified as “agricultural weeds” and species that were not agricultural weeds in the United Arab Emirates. When compared to plots in the open, P. cineraria canopies were associated with lower richness and density of non-weeds while having no impact on agricultural weed species. In contrast, there was lower richness and densities of non-weeds under canopies of P. juliflora, but higher densities of agricultural weeds than in the open surrounding the canopies. These patterns associated with Prosopis congeners and understory plant community composition might be due to the much higher litter deposition, if litter is inhibitory, and shallow root biomass under P. juliflora, or the different soil properties that corresponded with the two Prosopis canopies. In general, soils contained more nitrogen under P. juliflora than P. cineraria, and both understories were more fertile than soil in the open. Our results suggest that evolutionary history may play a role in how exotic invasive species may select for some traits over others in plant communities, with an exotic invader potentially creating reservoirs of agricultural weeds.