Boreal peatlands store substantial soil carbon and differ strongly in greenhouse gas exchange depending on factors such as hydrology and vegetation. Understanding these differences is increasingly important because many boreal peatlands are undergoing fen-to-bog transitions, potentially altering ecosystem carbon cycling and greenhouse gas exchange. We compared active-season (May–October) carbon dynamics between an oligotrophic sedge fen and an ombrotrophic patterned bog located 1.2 km apart within the Siikaneva wetland complex, southern Finland. We analysed fluxes of carbon dioxide (CO<sub>2</sub>) and methane (CH<sub>4</sub>) at diurnal, seasonal, and interannual scales, using eddy covariance measurements from 2011–2016. These fluxes were related to abiotic and biotic drivers, including soil temperature, photosynthetically active radiation, water table depth, and vascular plant leaf area index (LAI), with a focus on aerenchymatous LAI (LAI<sub>Aer</sub>).</p> <p>Across the six-year period both ecosystems acted as CO<sub>2</sub> sinks during the active-season and the fen was generally a stronger sink (mean±std NEE -80.8±42.1 g C m<sup>-2</sup> season<sup>-1</sup>) than the bog (-72.2±22.5 g C m<sup>-2</sup> season<sup>-1</sup>). The fen also exhibited higher gross primary production (GPP) and light-use efficiency, consistent with its higher total LAI, indicating vegetation structure and phenology as key drivers of the CO<sub>2</sub> sink difference under shared climate. CH<sub>4</sub> emissions were substantially higher at the fen (mean±std CH<sub>4 </sub>10.8±2.3 g C m<sup>-2</sup> season<sup>-1</sup>) than the bog (7.9±1.4 g C m<sup>-2</sup> season<sup>-1</sup>). CH<sub>4</sub> fluxes scaled positively with total LAI and LAI<sub>Aer</sub>, supporting the role of substrate supply and plant-mediated transport.</p> <p>The contrasting carbon dynamics between these adjacent peatland types suggest that ongoing fen-to-bog transitions may alter active-season carbon exchange by reducing CO<sub>2</sub> uptake and CH<sub>4</sub> emissions as vegetation composition and hydrological conditions shift toward bog-like states. Our results additionally indicate greater temporal variability in carbon fluxes at the fen than the bog. These findings highlight the importance of representing vegetation composition and canopy development in peatland models, rather than relying solely on peatland type.