This study provides the first complete framework for the valuation of several ecosystem services of agroforestry and uses a tree-based intercropping (TBI) system in southern Québec, Canada, as a case study to evaluate and monetize ecosystem services. Ten ecosystem services were estimated, all of which were of interest and directly applicable to most agricultural systems worldwide: nutrient mineralization, water quality, soil quality, pollination, biological control, air quality, windbreak, timber provisioning, agriculture provisioning, and climate regulation. A mix of mathematical models for the quantification and economic valuation of various ecosystem services were used. The results of the marginal analysis of all TBI ecosystem services revealed a total annual margin of 2 645 CAN$ ha^-1y^-1 (averaged over 40 years). The economic value of combined non-market services was 1 634 CAN$ ha^-1y^-1, which was higher than the value of marketable products (i.e. timber and agricultural products). An analysis of the present value of ecosystem services for a rotation of 40 years suggested that the provision of agricultural products ranked highest among the ecosystem services taken singly, followed by water quality, air quality, climate regulation, and soil quality. Total economic value of all ecosystem services for the rotation period was 54 782 CAN$ ha^-1, only one third of which was contributed by agricultural products. However, although the benefits of the ecosystem services provided by TBI were higher, farmers only benefited from agricultural products and timber. Thus, government incentives are needed to interest and compensate farmers in adopting practices that benefit society as a whole.