The agri-food sector plays a pivotal role in global sustainability efforts due to its significant environmental impacts, particularly in greenhouse gas emissions. Among its sub-sectors, the production and export of wine labeled as Protected Designation of Origin (PDO) or Protected Geographical Indication (PGI) presents both opportunities and challenges in reducing the carbon footprint of small and medium-sized enterprises (SMEs). This study quantifies the carbon footprint of PDO/PGI wine production and international distribution for a representative SME winery based in Laconia, Greece, over the period of 01/01/2023 to 31/12/2023. Using established carbon accounting protocols and life cycle assessment (LCA) principles, data were collected across the full production and supply chain, including vineyard operations, winemaking, packaging and road transport to domestic and retail destinations. The analysis revealed a total gross cradle-to-retail emissions of 443.631 kg CO₂-eq per year (1.11 kg CO₂-eq per bottle), while accounting for vineyard carbon sequestration (−550.375 kg CO₂-eq/year) resulted in a net carbon balance of −106.744 kg CO₂ per year, (−0.27 kg CO₂-eq per bottle). The largest emission contributor was road transportation. These findings demonstrate the potential for climate-neutral or even climate-positive wine production under specific conditions. This case study provides a replicable methodology for other SMEs in the agri-food sector seeking to measure and reduce their environmental footprint. It also highlights the value of PDO/PGI frameworks not only in preserving quality and origin but also in promoting sustainability and carbon accountability across agricultural value chains.