Companies are gradually becoming conscious about the necessity of reducing their environmental impact and adopting low-carbon strategies in order to cope with increasing institutional and social demands. However, remaining competitive while reducing the environmental impact and improving the corporate image requires adopting sophisticated mechanisms boosting eco-efficiency and keeping costs tight. Material Flows Cost Accounting (MFCA) is an instrument that allows the monitoring of, measurement of, and accounting for physical and monetary processes along the production process. If extended to the supply chain, and applied to the energy usage and CO2 emissions, it allows one to account for the Carbon Footprint (CF) of a company and its products at any given stage of the value chain. The current paper presents a case study developed under the framework of a three-year project to introduce an energy use and carbon emissions monitoring and accounting system in a large winery company in Spain, based on the MFCA approach and CF accountability. Including the supply chain of the company and the whole farming cycle of its main input, the case study presents the method and phases adopted to implement the project, its direct and indirect results and outcomes, and the conclusions that can be extracted, which may be inspirational for practitioners and scholars envisaging similar projects.