Ecologists still have to elucidate the complex feedback interactions operating among biodiversity and ecosystem processes in engineered systems. To address this, a field experiment was conducted to mimic natural mussel bed meta-ecosystems (Mytilus spp.) of the lower St. Lawrence Estuary (Quebec, Canada) and partition the effects of their biotic and abiotic properties and spatial structure on ecosystem processes and community dynamics of associated macro-invertebrates. We found positive intraspecific feedbacks between mussels and their recruits, and negative interspecific feedbacks between mussels and their associated ecosystem. These feedbacks were associated with mussel bed ecosystem processes (fluxes of ammonium and oxygen). In addition, we showed that proximity between mussel patches increased within-patch nutrient fluxes. Our study revealed the potential for meta-ecosystem engineering to drive feedback interactions between community and ecosystem functioning in marine fragmented systems. It also shows the relevance of meta-ecosystem theories as a conceptual framework to elucidate biotic and abiotic processes controlling ecosystem and community structure. Such framework could contribute to ecosystem-based management of spatially structured systems such as reserve networks and fragmented ecosystems.