Global climate change includes rising temperatures and increased pCO2 concentrations in the ocean, with potentially deleterious impacts to marine organisms. In a four-week climate change mesocosm simulation, I tested the effects of elevated temperature, elevated carbon dioxide and future conditions (a combination of both temperature and carbon dioxide) on the microbiomes of an important foundation species, the giant kelp Macrocystis pyrifera, and the surrounding water column. The water and kelp microbiome responded differently to each of the climate stressors. In the water microbiome each condition caused an increase in a distinct microbial order, whereas the kelp microbiome exhibited a reduction in the dominant symbiont, Alteromondales. The water column microbiomes were most disrupted by elevated pCO2, as demonstrated by a significant increase in species richness (ANOVA, p _ 0.01) and a four-fold increase in Rhizobiales. Kelp growth was negatively associated with elevated temperature, with a 20 fold increase in Flavobacteriales and increase in degradation enzymes capable of metabolizing kelp derived alginate, sucrose, and sulfatases. In contrast, kelp growth was positively associated with future conditions, with a 28-fold increase in Planctomycetales. I demonstrate novel interplay between an important macroalgal host and its microbiome that is strongly impacted by climate change perturbations.