Ocean acidification (OA) is a consequence of the global environmental changes that are occurring in the last decades. Acclimatization to OA is crucial for the survival of many benthic marine species, such as corals. Corals live in close association with endocellular photosynthetic symbionts and with complex communities of microorganisms (i.e. microbiomes) inhabiting their different anatomic compartments, and contributing to the host fitness and survival under environmental stress. Here we focus on the microbiomes associated to the surface mucus, soft tissue and skeleton of the widely distributed Mediterranean coral Balanophyllia europaea, growing along a pH gradient generated by an underwater CO2 seep close to Panarea island (Italy). Coral samples were taken at three sites along the gradient, mimicking the seawater conditions projected for 2100 under different IPCC scenarios. We used shotgun metagenomics and functional assignation of the reads to KEGG pathways and orthologs to report an acidification-induced functional rearrangement in the microbiomes genetic potential that could be able to mitigate the sub-optimal environmental conditions at three levels: i. acidification selects bacteria genetically equipped with functions related to stress resistance, at the mucus level ii. acidification induces shifts in the microbial carbohydrate metabolism from energy production to maintenance of the integrity of cell membranes and walls, as demonstrated by changes in relative abundance of pathways related to peptidoglycan and lipopolysaccharide biosynthesis iii. acidification promotes the gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. Our metagenomic study proposes a model for OA tolerance in a temperate coral relevant for the Mediterranean benthic ecosystem, besides remarking the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will be able to maintain their functionality under forthcoming acidified conditions.