This paper addresses a pragmatic and well-articulated qualitative methodology for the identification, prioritization, and consultation of stakeholder groups for a higher education institution as a key element for the organization in the context of digital transformation and Industry 5.0. First, the identification phase required technological surveillance and competitive intelligence, which allowed for defining the organization’s stakeholders and their characteristics. Then, the prioritization phase was performed to determine the stakeholders that potentially will have the greatest impact on achieving the institution’s strategic objectives to the targets of the Sustainable Development Goals prioritized by the institution, and those who will be most affected (positively or negatively) by the HEI activities. Finally, different methods and technological tools were used for consulting internal and external stakeholders, according to the type of relationship with each group, which allowed the understanding of the perceptions of different stakeholder groups on issues such as gender equity, mental health, regenerative economy, and diversity training. The results are then presented in terms of organizational context, where the concept of stakeholder group was defined by the dynamics of the selected HEI; the prioritized stakeholders include students, employees, academic and research sector, public sector, business sector, social sector, community, archdiocese and diocese, alumni, donors, and benefactors. This approach enabled the identification of issues that became a priority in the university’s actions towards the future. Although the presented methodology is mainly qualitative, which can represent a high degree of subjectivity, the stakeholder prioritization exercise provides organizations with inputs for decision making aligned with their needs and expectations. Using such a methodology can help the organization to experience structural changes reflected in improved strategic alignment, understanding, and satisfaction of stakeholders’ expectations and needs, enhancement of reputation, risk and conflict mitigation, and the consolidation of long-term healthy and trustworthy relationships, in the context of Society 5.0, where human-centered solutions are expected.