It remains uncertain how the net ecosystem CO2 exchange (NEE) of diverse peatlands will respond to warming. Here we compare five years of eddy covariance measurements of NEE and estimates of gross primary productivity and ecosystem respiration between a fen dominated by deciduous vegetation and an adjacent bog with evergreen vegetation in the Canadian Hudson Bay Lowlands. At the bog, daily net CO2 uptake lasted from snowmelt to snow cover onset, while at the fen, net CO2 uptake was delayed in spring and ended earlier in fall. Greater midsummer net CO2 uptake at the fen compensated for shoulder season net CO2 losses resulting in similar annual NEE at the two sites (fen: −52 ± 16 g C m−2, bog: −80 ± 14 g C m−2). Observations of a satellite-based productivity index also suggest lower shoulder season and higher peak vegetation productivity at these deciduous versus evergreen plant-dominated peatlands. The response of NEE to warmer weather differed between sites. Warming during the shoulder seasons increased net CO2 uptake at the evergreen plant-dominated bog, while it increased net CO2 losses at the fen where deciduous leaves had not yet emerged or had senesced. In contrast, warmer weather during the peak growing season appeared to reduce net CO2 uptake more at the bog than the fen resulting from both increasing ecosystem respiration and decreasing gross primary productivity. In the short term, warming will likely decrease annual net CO2 uptake of these and similar peatlands, although the magnitude will depend on factors including vegetation dynamics and seasonality of warming.