Since agriculture directly contributes to global anthropogenic greenhouse gas (GHG) emissions, integrating trees into agricultural landscapes through agroforestry systems is a viable adaptive strategy for climate change mitigation. The objective of this study was to evaluate the carbon (C) sequestration and financial benefits of C sequestration according to Quebec’s Cap-and-Trade System for Greenhouse Gas Emissions Allowances (C & T System) or the Système de plafonnement et d’échange de droits d’émission de gaz à effet de serre du Québec (SPEDE) program for two experimental 10-year-old tree-based intercropping (TBI) systems in southern Quebec, Canada. We estimated total C stored in the two TBI systems with hybrid poplar and hardwoods and adjacent non-TBI systems under agricultural production, considering soil, crop and crop roots, litterfall, tree and tree roots as C stocks. The C sequestration of the TBI and adjacent non-TBI systems were compared and the market value of the C payment was evaluated using the net present value (NPV) approach. The TBI systems had 33% to 36% more C storage than adjacent non-TBI systems. The financial benefits of C sequestration after 10 years of TBI practices amounted to of $2,259–$2,758 CAD ha⁻¹ and $1,568–$1,913 CAD ha⁻¹ for St. Edouard and St. Paulin sites, respectively. We conclude that valorizing the C sequestration of TBI systems could be an incentive to promote the establishment of TBI for the purpose of GHG mitigation in Quebec, Canada.