Background: After implementing the Tuning Educational Structures in Europe Project, numerous efforts have been made to define, establish, and evaluate nursing competences. The European Federation of Nurses Association played a key role in enacting the nursing competences included in Directive 2013/55/EU. Nevertheless, assessing competences remains elusive, and there is little research into nurses’ perceptions of the competency training provided by their universities. The purpose of the study was to explore the perceptions and experiences of newly qualified nurses about the competences they acquired during their university education. Methods: A qualitative research study was developed in a Spanish university. Twelve semi-structured interviews with newly qualified nurses were conducted, and two focus groups made up of twelve students were carried out in order to triangulate the results. Participants were recruited through email contact. Interviews focused on clinical training, theoretical content, and the reality of healthcare. Data was analyzed thematically. Results: Two main themes emerged: (1) improving theoretical content and (2) rethinking practical lessons and clinical training. A lack of knowledge about mental health, pharmacology, or critical care has been found; in addition, it was highlighted, among others, the need to improve communication skills in difficult and conflictive situations. Conclusions: Considering the participants’ perception of deficiency in some aspects of most of the competences established by the European Federation of Nurses Association, further research has been suggested to include other stakeholders’ views.