Introduction The Coronavirus Disease 2019 (COVID-19) pandemic placed enormous pressure on healthcare systems around the world, but it also provided valuable insights for healthcare organizations during this challenging period. Objective This study aimed to explore nurses’ lived experiences of vulnerability in hospital nursing management during the COVID-19 pandemic, and reflect on the lessons learned. Methods In this phenomenological study, 14 participants, including nurse managers at different levels and staff nurses, were selected by purposive sampling from one center university hospital. Data collection was done through in-depth individual semistructured interviews with participants and a review of weekly reports of crisis management meetings at the university hospital. Interviews were analyzed using Colaizzi's method in seven phases by MAXQDA software Version 10. Results One overarching theme, four themes, and 15 subthemes were obtained from analyses of interviews. Four themes of “nurses’ attrition,” “distrust of society to the organization,” “fragility in the organization's performance,” and “intensified inequalities” were extracted as threats to nursing management at the hospital. Subsequently, the weekly reports of crisis management meetings at the university hospital were analyzed to extract the solutions and lessons. Conclusion The unpreparedness of the healthcare system against a crisis can led to the loss of organizational assets, including medical staff and the credibility of the healthcare system. Limitations of the infrastructure at hospital became more obvious during the pandemic and caused serious threats to the healthcare system. Despite severe challenges along with the pandemic, it offered four valuable lessons in nursing management.