The forest sector can help reduce atmospheric CO2 through carbon (C) sequestration and storage and wood substitution of more polluting materials. However, climate change can have an impact on the C fluxes we are trying to leverage through forestry. We calculated the difference in CO2 eq. fluxes between ecosystem-based forest management and total forest conservation in the context of the temperate-boreal forest ecotone of Quebec (Canada), taking into account fluxes from forest ecosystems, wood product life cycle, and the substitution effect of wood products on markets. Over the 2020–2120 period, in the absence of climate change, ecosystem-based forest management and wood production caused average net annual emissions of 66.9 kilotonnes (kt) of CO2 eq. year−1 (relative to forest conservation), and 15.4 kt of CO2 eq. year−1 when assuming a 100% substitution effect of wood products. While management increased the ecosystem C sink, emissions from degradation of largely short-lived wood products caused the system to be a net source. Moreover, climate warming would decrease the capacity of ecosystems to sequester C and cause a shift towards more hardwood species. Our study highlights the need to adapt the industrial network towards an increased capacity of processing hardwoods into long-lived products and/or products with high substitution potential.