We measured the net ecosystem exchange (NEE) and respiration rates and modeled the photosynthesis and respiration dynamics in a cutover bog in the Swiss Jura Mountains during one growing season at three stages of regeneration (29, 42, and 51 years after peat cutting; coded sites A, B, and C) to determine if reestablishment of Sphagnum suffices to restore the C-sequestration function. From the younger to the older stage Sphagnum cover increased, while net primary Sphagnum production over the growing season decreased (139, 82, and, 67 g m−2 y−1 for A, B, and C respectively), and fen plant species were replaced by bog species. According to our NEE estimations, over the vegetation period site A was a net CO2-C source emitting 40 g CO2-C/m2 while sites B and C were accumulating CO2-C, on average 222 and 209 g CO2-C/m2, respectively. These differences are due to the higher respiration in site A during the summer, suggesting that early regeneration stages may be more sensitive to a warmer climate. Methane fluxes increased from site A to C in parallel with Eriophorum vaginatum cover and vascular plant leaf area. Our results show that reestablishing a Sphagnum cover is not sufficient to restore a CO2-sequestrating function but that after circa 50 years the ecosystem may naturally regain this function over the growing season.