Nowadays, organizations are shifting towards project-based management strategies in order to implement more flexible structures that allow them to respond and compete in complex business environments. In this way, project management has been regarded as a valuable competence, providing the organization and its management teams the opportunity to adapt the knowledge, skills and tools necessary to meet project requirements as well as organizational goals. Among the wide array of decisions project managers have to evaluate project selection (PS) and project prioritization (PP) are crucial in order to maximize stakeholder’s value through the effective management and allocation of resources to projects that are in alignment with the organization’s strategic objectives. Moreover, the integration of management techniques, guidelines and practices has also become a necessity for intergovernmental (IGOs) and non-profit organizations (NPOs), especially because they do not possess a conventional bottom line and in most instances, their main goal is rarely profit maximization. Although the main objective of operations of IGOs and NPOs is also success, this is difficult to be defined and evaluated. As a matter of fact, studies related to project management in IGOs and NPOs argue that the literature available has ignored the public good sector to a great extent, since the majority of the portfolio management tools available are tailored for commercial and for-profit organizations (FPOs). Consequently, this study explores the project portfolio management (PPM) process in intergovernmental and non-profit organizations focusing specifically on the decision-making process regarding project selection and prioritization. It provides an understanding of the main criteria these organizations take into consideration when selecting and prioritizing projects and the impact these methodologies have in terms of achieving project and organizational success. In addition, it examines the role of the project management office (PMO) and individual project managers based on their influence on the decisions concerning project selection and prioritization, as well as project success and organizational success. The key findings of this study confirm the relevance of the priorities determined by the main stakeholders as one of the principal criteria for project selection, followed by the allocation of funding and resources and the need for strategic alignment. Furthermore, in terms of determining a ranking among the selection criteria, this study has found that within these organizations all the different requirements encompassed in the selection process should be treated as equal. Additionally, it has been possible to determine that for intergovernmental and non-profit organizations the project selection and project prioritization phases are not isolated from one another; and are in fact treated as on single criteria. Conversely, the findings of this study contradict the proposition that the project management office is highly influential in the decision-making process of IGOs and IGOs; however, it emphasizes the role of the project manager in project and organizational success as highly valuable since they possess the hard and soft project management skills that increase the chances to achieve the organizational goals.