Within the framework of the project “Real-time environmental assessment of agricultural and agrifood production for the support of certification schemes”, a real-time, web-based Life Cycle Assessment (LCA) tool has been developed. To demonstrate the tool’s functionality, the environmental impacts of four different wheat production routes were assessed. Emphasizing a circular economy approach in the agricultural sector can reduce waste, produce bioenergy, and reduce the overall environmental footprint. Despite this potential, there is an increased uncertainty regarding bioenergy output and electricity consumption of various small-scale technologies. Therefore, within the scope of the project, laboratory-scale experiments were conducted to evaluate the production of biofuels using wheat residues and wastes. The waste-to-energy technologies that were included are an oil press, a pellet mill, and an ethanol still. This study presents the results of the lab-scale production of biodiesel, bioethanol, and pellets. Finally, the potential reduction in Global Warming Potential (GWP) that can be achieved by the integration of waste-to-energy in wheat production was quantified.