Abstract Background Among the processes to be experienced by any organization during its establishment is the formation of an organizational identity. This process can be understood as the activity and event through which an organization becomes unique in the mind of its members. An organizational identity leads to an identification and both are directly associated with the success of an institution. This study is about a public higher education institution in health in its early years, with distinctive characteristics in the country where it is situated. In spite of having been successful in the graduation of its students it has fragile institutional bases, lack of autonomy and internal problems common to other institutions of this type. Thus, this study was conducted to understand how this institution defined itself among its own members, the elements of its identity and what justified its relative success despite its weaknesses. Methods A mixed-method approach was used to evaluate how a representative portion of this organization identifies with it. For the qualitative study two focus groups were conducted with transcripts submitted to content analysis proposed by Bardin, culminating in results from which a Likert scale-based questionnaire was elaborated and applied to 297 subjects. Results There were six central elements of the organizational identity made evident by the focus groups: political / ideological conflict; active teaching and learning methodologies; location / separation of campuses; time of existence; teaching career; political-administrative transformations. The quantitative analysis revealed in more detail the general impressions raised in the focus groups. Most results were able to demonstrate distinct identifications of the same identity with its exposed weaknesses. Conclusions Lack of autonomy, administrative and structural shortcomings and ideological or political conflicts presented themselves as problems capable of destabilizing the identity of a public higher education institution. On the other hand, one way to combat such problems is through the development of the institution itself, particularly by becoming more active and useful to the community and seeking in a common interest to the higher administration agencies.