Recent literature has recommended that life cycle assessments (LCA) of forest bioenergy supply chains consider the impact of biomass harvest on ecosystem carbon stocks as well as the net emissions arising from combustion of various forms of biofuels compared with reference fossil fuel systems. The present study evaluated the magnitude and temporal variation of ecosystem C stock changes resulting from harvest of roadside residues and unutilized whole trees for bioenergy. The Carbon Budget Model (CBM-CFS3) was applied to the Gordon Cosens Forest, in northeastern Ontario, along with the Biomass Opportunity Supply Model (BiOS-Map), for cost analysis of different types of biomass comminution. Natural gas (NG) steam and electricity, grid electricity, and coal electricity reference systems were analyzed for a pulp and paper mill. The findings showed that the forested landscape becomes a net sink for carbon following the 20th year of roadside residue harvest, compared to whole-tree harvest, where the forested landscape remained a net source of carbon over the entire 100 year rotation. The cumulative ecosystem carbon loss from whole-tree harvest was 11 times greater compared to roadside residue harvest. BiOS-Map analysis suggested that due to technical and operational limits, between 55%-59% and 16%-24% of aboveground biomass was not recovered under roadside residue and whole-tree harvest respectively. The cost of delivering roadside residues was estimated at $52.32/odt–$57.45/odt, and for whole trees $92.63/odt–$97.44/odt. The Life Cycle Assessment (LCA) analysis showed break-even points of 25, 33 and 6 years for roadside residues displacing NG steam, NG electricity, and coal, respectively. No GHG reduction was achieved when forest biomass was used to displace grid electricity that is generated in Ontario. Whole-tree bioenergy resulted in no GHG reduction for NG displacement, and a break-even point of 70-86 years for coal. A net GHG reduction of 67% and 16% was realized when roadside residues and whole trees were used to displace coal, compared to 45% and 38% when roadside residues were used to displace NG steam and NG electricity, respectively. Therefore, it is recommended that bioenergy deployment strategies focus on the utilization of roadside residues, if the main goal is GHG mitigation.