Seagrasses support local fisheries and are culturally important to the Cocos Malay community in the Cocos (Keeling) Islands, but have suffered devastating declines likely due to multiple pressures (warming, increased turbidity with coastal development, and intense turtle grazing). Local knowledge combined with a three-year herbivore exclusion study has shown that ongoing grazing is likely restricting seagrass persistence in this coral atoll. Leveraging off this initial research, we aimed to assess how traits and function of seagrasses changed between areas protected from herbivory for three years using cages, and areas exposed to ongoing grazing. Caging was effective at protecting seagrass from grazing, and these plants had significantly greater leaf density and size compared to grazed plants. Photosynthetic rates per standard leaf area were similar irrespective of grazing history, however productivity was higher in cages when scaled to total leaf area. Our results indicate that grazing changes the structure and function of seagrass in one of Australia’s most remote territories. This research will inform restoration strategies to safeguard seagrass ecosystems in the newly declared Cocos (Keeling) Islands Marine Park. Future work is now exploring if natural structure in the lagoon can provide refuge from herbivory and maintain their function.