Biogenic volatile organic compounds (BVOCs) are major precursors of both ozone and secondary organic aerosols (SOA) in the troposphere and represent a non‐negligible portion of the carbon fixed by primary producers, but long‐term ecosystem‐scale measurements of their exchanges with the atmosphere are lacking. In this study, the fluxes of 46 ions corresponding to 36 BVOCs were continuously monitored along with the exchanges of mass (carbon dioxide and water vapor) and energy (sensible and latent heat) for an entire year in a poplar (Populus) short‐rotation crop (SRC), using the eddy covariance methodology. BVOC emissions mainly consisted of isoprene, acetic acid, and methanol. Total net BVOC emissions were 19.20 kg C ha−1 yr−1, which represented 0.63% of the net ecosystem exchange (NEE), resulting from −23.59 Mg C ha−1 yr−1 fixed as CO
2 and 20.55 Mg C ha−1 yr−1 respired as CO
2 from the ecosystem. Isoprene emissions represented 0.293% of NEE, being emitted at a ratio of 1 : 1709 mol isoprene per mol of CO
2 fixed. Based on annual ecosystem‐scale measurements, this study quantified for the first time that BVOC carbon emissions were lower than previously estimated in other studies (0.5–2% of NEE) on poplar trees. Furthermore, the seasonal and diurnal emission patterns of isoprene, methanol, and other BVOCs provided a better interpretation of the relationships with ecosystem CO
2 and water vapor fluxes, with air temperature, vapor pressure deficit, and photosynthetic photon flux density.