Our study showed how ocean acidification can exert both direct and indirect influences on the interactions among trophic levels within the microbial loop. Microbial grazer abundance was reduced at CO₂ concentrations at and above 634 µatm, while microbial communities increased in abundance, likely due to a reduction in being grazed. Such changes in predator–prey interactions with ocean acidification could have significant effects on the food web and biogeochemistry in the Southern Ocean.