Due to the increasing size of the population, society faces several challenges for sustainable and adequate agricultural production, quality, distribution, and food safety in the strategic project portfolio selection (SPPS). The initial adaptation of strategic portfolio management of genetically modified (GM) Agro by-products (Ab-Ps) is a huge challenge in terms of processing the agro food product supply-chain practices in an environmentally nonthreatening way. As a solution to the challenges, the socio-economic characteristics for SPPS of GM food purchasing scenarios are studied. Evaluation and selection of the GM agro portfolio management are the dynamic issues due to physical and immaterial criteria involving a hybrid multiple criteria decision making (MCDM) approach, combining modified grey Decision-Making Trial and Evaluation Laboratory (DEMATEL), Multi-Attributive Border Approximation area Comparison (MABAC) and sensitivity analysis. Evaluation criteria are grouped into social, differential and beneficial clusters, and the modified DEMATEL procedure is used to derive the criteria weights. The MABAC method is applied to rank the strategic project portfolios according to the aggregated preferences of decision makers (DMs). The usefulness of the proposed research framework is validated with a case study. The GM by-products are found to be the best portfolio. Moreover, this framework can unify the policies of agro technological improvement, corporate social responsibility (CSR) and agro export promotion.