Maritime Antarctica is one of the most stressful environments for plant life worldwide. However, two vascular plant species (Deschampsia antarctica and Colobanthus quitensis) have been able to colonize this hostile environment. Although it has been proposed that C. quitensis possesses tolerance mechanisms and adaptations allowing survival and growth under such stressful conditions, the underlying molecular/transcriptional mechanisms are currently unknown. Furthermore, the impact of global warming on the endophytic and epiphytic organisms associated with C. quitensis remains unclear. Here, a metatranscriptomic approach was used to determine the effect of an in situ simulated global warming scenario on C. quitensis plants. We found a large number of differentially expressed genes successfully annotated (2,997), suggesting that climate change modulates the metatranscriptome of C. quitensis plants and associated endophytes and epiphytes. Interestingly, 50.5% and 26.8% of up- and down-regulated genes, respectively, are from non-plant species (putative endophytic and epiphytic organisms, such as fungi). Interestingly, Gene Ontology analysis pointed out several biological processes differentially enriched in non-plant microorganisms associated with C. quitensis grown in a simulated global warming scenario. Taken together, these results suggest that climatic drivers are shaping plant-microorganism interactions, and that endophytes/epiphytes may play crucial roles in plant adaptation to extreme environmental conditions.