Plant communities play a key role in regulating greenhouse gas (GHG) emissions in peatland ecosystems and therefore in their ability to act as carbon (C) sinks. However, in response to global change, a shift from <i>Sphagnum</i> to vascular plant-dominated peatlands may occur, with a potential alteration in their C-sink function. To investigate how the main GHG fluxes (CO<sub>2</sub> and CH<sub>4</sub>) are affected by a plant community change (shift from dominance of <i>Sphagnum</i> mosses to vascular plants, i.e. <i>Molinia caerulea</i>), a mesocosm experiment was set up. Gross primary production (GPP), ecosystem respiration (ER) and CH<sub>4</sub> emission models were used to estimate the annual C balance and global warming potential under both vegetation covers. While the ER and CH<sub>4</sub> emission models estimated an output of, respectively, 376 and 7 gC m<sup>−2</sup> y<sup>−1</sup> in <i>Sphagnum</i> mesocosms, this reached 1018 and 33 gC m<sup>−2</sup> y<sup>−1</sup> in mesocosms with <i>Sphagnum rubellum</i> and <i>Molinia caerulea</i>. Annual modelled GPP was estimated at −414 and −1273 gC m<sup>−2</sup> y<sup>−1</sup> in <i>Sphagnum</i> and <i>Sphagnum</i> + <i>Molinia</i> plots, respectively, leading to an annual CO<sub>2</sub> and CH<sub>4</sub> budget of −30 gC m<sup>−2</sup> y<sup>−1</sup> in <i>Sphagnum</i> plots and of −223 gC m<sup>−2</sup> y<sup>−1</sup> in <i>Sphagnum</i> + <i>Molinia</i> ones (i.e., a C-sink). Even if, CH<sub>4</sub> emissions accounted for a small part of the gaseous C efflux (ca. 3 %), their global warming potential value makes both plant communities have a climate warming effect. The shift of vegetation from <i>Sphagnum</i> mosses to <i>Molinia caerulea</i> seems beneficial for C sequestration at a gaseous level. However, roots and litters of <i>Molinia caerulea</i> could provide substrates for C emissions that were not taken into account in the short measurement period studied here.