Ocean acidification is one of the main stressors affecting marine ecosystems. Rare CO2 vents offer a unique opportunity to investigate the response of benthic ecosystems to acidification. However, the benthic habitats that have been investigated so far are mainly very shallow water (≤5 m depth) and, therefore, to habitats that are poorly representative of the broad range of habitats that occur on the continental shelf. Here, we show that a decrease from pH 8.1 to 7.9 observed in a CO2 vent system at 40 m depth leads to a dramatic shift in highly diverse and structurally complex habitats. Forests of the kelp Laminaria rodriguezii usually found at larger depths (>65 m) replace the dominant habitats (i.e. coralligenous outcrops and rhodolith beds), which are mainly characterized by calcifying organisms. Only the aragonite-calcifying algae are able to survive in acidified waters, while high-magnesium calcite organisms lack almost completely. Beyond significant changes at species level also reported in most of previous studies, our results demonstrate that moderate ocean acidification and pH levels expected to occur at the end of this century will entail outstanding changes in the distribution and dominance of key benthic ecosystems at regional scales, with far-reaching ecological and socio-economic implications.