Although there is mounting evidence that biodiversity is an important and widespread driver of ecosystem multifunctionality, much of this research has focused on small-scale biodiversity manipulations. Hence, which mechanisms maintain patches of enhanced biodiversity in natural systems and if these patches elevate ecosystem multifunctionality at both local and landscape scales remain outstanding questions. In a 17 month experiment conducted within southeastern United States salt marshes, we found that patches of enhanced biodiversity and multifunctionality arise only where habitat-forming foundation species overlap—i.e. where aggregations of ribbed mussels ( Geukensia demissa ) form around cordgrass ( Spartina alterniflora ) stems. By empirically scaling up our experimental results to the marsh platform at 12 sites, we further show that mussels—despite covering only approximately 1% of the marsh surface—strongly enhance five distinct ecosystem functions, including decomposition, primary production and water infiltration rate, at the landscape scale. Thus, mussels create conditions that support the co-occurrence of high densities of functionally distinct organisms within cordgrass and, in doing so, elevate salt marsh multifunctionality from the patch to landscape scale. Collectively, these findings suggest that patterns in foundation species' overlap drive variation in biodiversity and ecosystem functioning within and across natural ecosystems. We therefore argue that foundation species should be integrated in our conceptual understanding of forces that moderate biodiversity–ecosystem functioning relationships, approaches for conserving species diversity and strategies to improve the multifunctionality of degraded ecosystems.