Food systems account for one third of greenhouse gas emissions while fish production is assigned 4% of total anthropogenic emissions as well as other environmental implications. The Greek fishery industry is a very promising and upcoming sector with renowned products such as “Avgotaracho Mesolongiou”, the Greek bottarga, which is a product of designated origin (PDO) with cultural and economic significance but unexplored environmental impacts. The aim of the study is to depict the environmental hot-spots of “Avgotaracho Mesolongiou” production using the life cycle analysis (LCA) methodology with the help of SimaPro v3.5 software and the Ecoinvent database v3.9. “Avgotaracho Mesolongiou” supply chain is divided into the fish extraction, roe processing and transport, and retail stages, while the inventory of each stage is filled with data depicted from producers via a questionnaire and findings from the literature. The hot-spot analysis of Avgotaracho Mesolongiou exhibited high human carcinogenic toxicity, and marine and freshwater ecotoxicity impacts that account for more than 90% of total normalized scores. More specifically, the use of metallic traps in the fish-catching facilities presented the highest contribution among the inputs and was responsible for more than 70% of total normalized scores. Furthermore, the uncontrolled treatment processes of waste streams are attributed 6% of total normalized scores. More specifically, waste wood open-burning accounts for 10% of human carcinogenic toxicity while disposal of wastewater was responsible for 25% of freshwater eutrophication. Moreover, a scenario-driven LCA was conducted to compare the existing waste treatment meth+ods to a proposed improved waste management (IWM) scenario. The implementation of controlled treatment processes resulted in a decrease in human carcinogenic toxicity and freshwater eutrophication impact by 8% and 26%, respectively. The outcome was proven to be robust in respect to the affected impact categories while the fish extraction remains the most impactful stage of the supply chain when subjected to a sensitivity analysis.