Canadian agricultural and forestry systems are required to contribute to achieving net-zero greenhouse gas emissions by 2050. However, these systems focus on strategies that can only reduce a fraction of their emissions. In this thesis, a series of studies were conducted to obtain a holistic view of opportunities to better manage the flows of energy and carbon associated with the agri-food and forestry systems of Canada towards achieving the net-zero emission target. First, using data obtained from government sources and the literature, a comprehensive model was created to quantify and compare the flows of energy and carbon associated with the agri-food system and those associated with crude oil-refined petroleum products systems. Results of this study suggest that about 86% of energy and carbon associated with Canada’s agri-food system is embedded in wastes and residual biomass that are usually left to decompose, thereby returning carbon as carbon dioxide (CO2) into the atmosphere. The second study developed a methodology to calculate the 100-year global warming impact associated with diverting residual lignocellulosic biomass from business-as-usual scenarios (decomposition in agricultural, forestry, or landfill sites) into bioenergy use. The results showed that the CO2 released from bioenergy diversion has a global warming potential (GWPbio, units of kg CO2e/kg CO2) that is >0 and could be as high as 0.97 (the GWP for fossil CO2 emissions is 1.0) if the biomass decomposition is slow as in the case of wood in landfills. A third study added the biogenic CO2 analysis to an assessment of life cycle greenhouse emissions associated with co-firing lignocellulosic residual biomass with natural gas to produce one megagram of clinker in a cement plant. Although the co-firing scenario reduced natural gas emissions by 23%, it increased the total energy inputs and emissions associated with clinker production by about 18% and 10%, respectively, relative to the reference scenario. The thesis recommends that policy and investment decisions aimed at achieving net-zero emissions in the agri-food and forestry sectors should consider all anthropogenic flows of energy and carbon, and care should be taken if residual biomass is to be diverted for use as a bioenergy feedstock.