The paper focuses on a new theoretical-methodological approach to interpreting functional transformation processes of farms located in rural areas and marked by a delay in development. We have defined a theoretical paradigm of optimal value portfolio (OVP) which considers -in a new light- multifunctional agricultural farms as an ensemble of governance structures optimizing the creation of value. The need to validate the OVP functionality has led us to identify a new methodological approach referred to as the Value Portfolio and Multifunctional Governance Analysis (VPMGA). This analysis embeds value chain analysis and governance value analysis and at the same time attempts to overcome the “sectoral” limits representing also a new and further development. We deem, in fact, that the VPMGA best responds to the specificities of multifunctional agricultural farms. Through the VPMGA we have identified four determining family variables which are internal and external to the farm (internal resources, market, territory, policies). We have also assessed the functional links with the boundary shift processes and the mechanisms governing transactions and the creation of an optimal value portfolio. We have empirically verified this approach on selected agro-food chains which are located in rural areas characterized by different levels of development. From the findings we have defined various ideal types of farms that allowed us to make future scientific assumptions and highlight normative implications for improving managerial decision-making processes based on the VPMGA model. In this way, the VPMGA can be a tool to inform policy makers, especially in the light of the new challenges facing rural development.