Invasive species pose a significant threat to biodiversity, particularly in arid ecosystems where extreme environmental conditions limit the capacity for rapid vegetation recovery. Buffelgrass (Cenchrus ciliaris), introduced from South Africa for livestock forage, has become one of the most detrimental invasive species throughout the Sonoran Desert. This species is known to begin its invasion process in native desertscrub beneath the canopy of trees, sometimes recognized as nurse plants. We investigated how buffelgrass invasion affects plant and soil microbial communities under contrasting desert conditions in central Sonora, Mexico. Specifically, we compared open areas (i.e., bare, with natives, and with buffelgrass) and areas beneath the canopy of three nurse tree species (i.e., mesquite, ironwood, and palo verde), with and without buffelgrass invasion, in two neighboring sites which differed in cover type: one, a deliberately planted buffelgrass pasture (transformed site) and the other, a desertscrub naturally invaded by buffelgrass (native site). Our results show that the transformed site exhibited higher plant species richness, along with a larger proportion of invasive and ruderal species. Cover type emerged as the primary factor influencing the richness and composition of soil microbial communities. Interestingly, our findings suggest that nurse trees (in particular, palo verde) may help mitigate the impact of buffelgrass in semi-arid ecosystems.