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The present paper embarks on an investigation of the main risks associated with agri-food supply chains. A total of 11 key risks, namely Natural disasters of a global or local scale; Workers’ strikes; Change in government regulations or safety standards; Supply chain disruptions due to social or political unrest; Short term raw materials or products (expiration issue); Seasonality; Food safety incidents; Lack of smooth interconnection with other chain participants and Market and pricing strategies, economic crises and seven root risks (Natural disasters of a global or local scale; Workers’ strikes; Change in government regulations or safety standards; Rapid deterioration of raw materials (expiration) due to seasonality; Food safety incidents; Fraud in the food sector; Market and pricing strategies, economic crises) are applicable to all four stages of the agri-food supply chains were identified. An expert survey together with the Best-Worst Multi Criteria Decision Making method was employed as the main research tools. The most important root risks for agri-food supply chains are natural disasters of a global or local scale; workers’ strikes; change in government regulations or safety standards; rapid deterioration of raw materials (expiration), seasonality; food safety incidents; fraud in the food sector; market and pricing strategies economic crises. The most appropriate risk mitigation measures for each of the root risks were derived and assessed.