Agricultural sector should be considered, as one of the main economic development sectors in the entire world, while at the same time is responsible for important pollution. The life cycle assessment (LCA) procedure was involved in the agricultural strategic development planning for Balkan region, as a useful tool to identify and quantify potential environmental impacts from the production of apple juice, wine and pepper pesto in three selected sites in Greece, North Macedonia and Bulgaria. These three products were chosen, as are considered as the main economic activities at the areas. The LCA approach covered the entire production line of each product. Based on the LCA results, which comprise the size of six impact categories characterization factors, suggestions were made in order to minimize the footprint of the apples orchard, vineyard and pepper cultivation plots as well as of the production processes of apple juice, wine and pepper pesto as final distribution products. The results indicate that changes in the cultivation and the production must be considered in order to optimize the environmental footprint. Moreover, the whole approach could be useful for agricultural stakeholders, policy makers and producers, in order to improve their products ecological performance, reduce food loss and food waste and increase the productivity of the agricultural sector, while at the same time can improve the three pillars of sustainability through strategy development.