Cultivation of bioenergy crops has been suggested as a promising option for reduction of greenhouse gas (GHG) emissions from arable organic soils (Histosols). Here, we report the annual net ecosystem exchange (NEE) fluxes of CO2 as measured with a dynamic closed chamber method at a drained fen peatland grown with reed canary grass (RCG) and spring barley (SB) in a plot experiment (n = 3 for each cropping system). The CO2 flux was partitioned into gross photosynthesis (GP) and ecosystem respiration (RE). For the data analysis, simple yet useful GP and RE models were developed which introduce plot-scale ratio vegetation index as an active vegetation proxy. The GP model captures the effect of temperature and vegetation status, and the RE model estimates the proportion of foliar biomass dependent respiration (Rfb) in the total RE. Annual RE was 1887 ± 7 (mean ± standard error, n = 3) and 1288 ± 19 g CO2-C m−2 in RCG and SB plots, respectively, with Rfb accounting for 32 and 22% respectively. Total estimated annual GP was −1818 ± 42 and −1329 ± 66 g CO2-C m−2 in RCG and SB plots leading to a NEE of 69 ± 36 g CO2-C m−2 yr−1 in RCG plots (i.e., a weak net source) and −41 ± 47 g CO2-C m−2 yr−1 in SB plots (i.e., a weak net sink). Standard errors related to spatial variation were small (as shown above), but more significant uncertainties were related to the modelling approach for establishment of annual budgets. In conclusion, the bioenergy cropping system was not more favourable than the food cropping system when looking at the atmospheric CO2 emissions during cultivation. However, in a broader GHG life-cycle perspective, the lower fertilizer N input and the higher biomass yield in bioenergy cropping systems could be beneficial.