Significance In the current changing climate, it is essential to improve crop production and resilience under dry and nutrient-poor conditions. Desert plants have naturally evolved to flourish under such conditions. Therefore, understanding the underlying mechanisms for their adaptation can potentially help to ensure food security. The Atacama Desert, the driest nonpolar place on Earth, offers a unique opportunity to explore plant adaptations to extreme environmental conditions. Here, we reveal how the adaptive strategies common or specific to the major plant lineages in the Atacama include enrichment of plant growth-promoting bacteria near their roots and positive selection of genes that are associated with key beneficial processes for plant survival. These strategies can potentially direct the molecular breeding or engineering of resilient crops.