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Funding Information: We thank A. Toikkanen and N. Uotila for their valuable work in the laboratory, and I. McDonald for field assistance. We thank two anonymous reviewers for their very constructive comments that helped improve this paper. The study was funded by the Academy of Finland (Project ID 294853) and the University of Helsinki and Stockholm University strategic fund for collaborative research (The Baltic Bridge initiative). DL and ST were supported by a senior visiting research fellowship funded by the Walter and Andrée de Nottbeck Foundation. Publisher Copyright: © 2022 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America. Coastal vegetated habitats such as seagrasses are known to play a critical role in carbon cycling and the potential to mitigate climate change, as blue carbon habitats have been repeatedly highlighted. However, little information is known about the role of associated macrofauna communities on the dynamics of critical processes of seagrass carbon metabolism (e.g., respiration, turnover, and production). We conducted a field study across a spatial gradient of seagrass meadows involving variable environmental conditions and macrobenthic diversity to investigate (1) the relationship between macrofauna biodiversity and secondary production (i.e., consumer incorporation of organic matter per time unit), and (2) the role of macrofauna communities in seagrass organic carbon metabolism (i.e., respiration and primary production). We show that, although several environmental factors influence secondary production, macrofauna biodiversity controls the range of local seagrass secondary production. We demonstrate that macrofauna respiration rates were responsible for almost 40% of the overall seafloor community respiration. Macrofauna represented on average >25% of the total benthic organic C stocks, high secondary production that is likely to become available to upper trophic levels of the coastal food web. Our findings support the role of macrofauna biodiversity in maintaining productive ecosystems, implying that biodiversity loss due to ongoing environmental change yields less productive seagrass ecosystems. Therefore, the assessment of carbon dynamics in coastal habitats should include associated macrofauna biodiversity elements if we aim to obtain robust estimates of global carbon budgets required to implement management actions for the sustainable functioning of the world's coasts.