Tree-based intercropping (TBI) system has been suggested as an alternative to conventional monocropping (CM) for decreasing overall greenhouse gas (GHG) emissions. However, little is known about the advantages of TBI compared with organic CM system with low fertilizer inputs. This project compared CO₂ and N₂O dynamics in replicated TBI and CM in Saint-Paulin (QC, Canada), established about 12 yr prior to this study under organic production, with horse manure and pruning residues as soil amendments. An experimental field, using a complete randomized block design, was instrumented in both systems. A five-point sampling transect was established between tree rows in each of the six plots. Surface CO₂ and N₂O fluxes, CO₂ and N₂O soil concentrations, and other physicochemical properties were analyzed at 0.125 and 0.25 m depths over two growing seasons. CO₂ and N₂O concentrations in TBI soil were similar to or lower than in CM soil. Lower CO₂ and N₂O emissions suggest that TBI would decrease overall GHG mitigation, even when compared with organic production with low fertilizer inputs, in addition to its potential for carbon sequestration in wood and other advantages that are not discussed in this study.