Anthropogenic climate change is driving ocean acidification which threatens the ecologically and economically significant Sydney rock oyster, Saccostrea glomerata (Gould, 1850). S. glomerata occurs naturally and is cultured in New South Wales estuaries which are acidifying at a greater rate than the global oceanic average. However, seagrass respiration may provide marine organisms refugia from such rapid acidification. This study aimed to determine if the seagrass Zostera muelleri sub spp. capricorni benefits the Sydney rock oyster S. glomerata, and if these benefits can modify any anticipated negative impacts of ocean acidification. Ambient and future ocean acidification conditions were simulated in 52 L mesocosms at ambient (381 μatm) and future (848 μatm) CO2, with and without Z. muelleri. Oyster growth, physiology and microbiomes of oysters and seagrass were measured. Seagrass was beneficial to oyster growth at ambient pCO2, but did not positively modify the impacts of ocean acidification on oysters at future pCO2. Oyster microbiomes were altered by the presence of seagrass but not by future pCO2. Together our results indicate seagrasses such as Z. muelleri may be a sustainable approach to ensure the continuation of S. glomerata aquaculture but may not be a panacea for the impacts of climate change.