Wetlands support unique biodiversity and play a key role in carbon cycles, but have dramatically declined in extent worldwide. Restoration is imperative yet often challenging to counteract loss of functions. Nature-based solutions such as the creation of novel ecosystems may be an alternative restoration approach. Targeted restoration strategies that account for the effects of vegetation on greenhouse gas (GHG) fluxes can accelerate the carbon sink function of such systems. We studied the relationships between vegetation, bare soil, and GHG dynamics on Marker Wadden in the Netherlands, a newly-created 700-ha freshwater wetland archipelago created for nature and recreation. We measured CO2 and CH4 fluxes, and soil microbial activity, in three-year-old soils on vegetated, with distinct species, and adjacent bare plots. Our results show that CH4 fluxes positively related to organic matter and interacted between organic matter and water table in bare soils, while CH4 fluxes positively related to plant cover in vegetated plots. Similarly, Reco in bare plots negatively related to water table, but only related positively to plant cover in vegetated plots, without differences between vegetation types. Soil microbial activity was higher in vegetated soils than bare ones, but was unaffected by substrate type. We conclude that GHG exchange of this newly-created wetland is controlled by water table and organic matter on bare soils, but the effect of vegetation is more important yet not species-specific. Our results highlight that the soil and its microbial community are still young and no functional differentiation has taken place yet and warrants longer-term monitoring