In the context of global energy shortage and climate change, developing local biogas plants coupled with agricultural systems can become an important strategy for cleaner rural energy and sustainable agriculture. In this research, a Life Cycle Assessment (LCA) method was applied to compare the climate impact of two essentially different systems: 1) Scenario I: an agricultural system based on the cultivation of 11 hectares of energy tobacco primarily for seed production; 2) Scenario II: a hypothetical Scenario Investigating the climate impact concerned with a crop variety – a higher yielding variety cultivated for both seed and biomass - and introducing biogas production. Both scenarios focus on the energy tobacco biomass residues. The overall aim of the study was to evaluate the climate impact of these two scenarios in the agricultural and energy system in Marble Hall, Limpopo Province, South Africa. The biogas was used for electricity production, replacing coal-based electricity on the grid. Biomass residues were chosen as feedstock for biogas production since this crop presently receives much attention in the region as the oily seeds can be used to produce sustainable jet fuel. Results from the modelling show that Scenario II would provide a positive climate impact: a 43% reduction of greenhouse gases compared to Scenario I. The higher yielding crop variety in Scenario II means that there is also potential to produce more sustainable jet fuel to replace conventional aviation fossil fuel. Taking this into account, the biogas scenario can reduce emissions by 79% compared to the base case. An analysis of the results indicates that there are several variables in the system model that are uncertain and sensitive to change, proving that more research is necessary to make robust conclusions about the validity of the presented results.