BACKGROUND: The mental well-being of university students has been a growing concern in Public Health and has been exacerbated by the COVID-19 pandemic. The pandemic (including the post-pandemic era) introduced and exacerbated a variety of potential stressors for vulnerable individuals and communities, resulting in an increase in mental health issues among university students. Resilience, as a process, is the ability of a system to adapt and grow in the face of adversity. This is a crucial aspect to consider when examining the coping of university students in critical situations such as COVID-19. OBJECTIVE: This study aims to assess the association between resilience and mental health outcomes among university students in Cyprus during the post-COVID-19 pandemic era. METHODS: A parallel embedded mixed methods research design will be utilized to assess resilience, measured by the Conner-Davidson Resilience Scale (CD-RISC), the COVID-19 Impact Scale (CIS) and mental health outcomes measured by the Symptom Checklist 90-Revised (SCL 90-R), during the COVID-19 post-pandemic era (January 2022-July 2024) among university students in the Republic of Cyprus. The study will be conducted in two stages: a pilot study followed by the main study. Quantitative data will be collected through a web-based survey, while qualitative data will be obtained through in-person focus groups designed to capture participants' experiences. Participants will be recruited using a proportional quota sampling approach to achieve representativeness based on predefined demographics. The study protocol has been approved by the Cyprus Bioethics Committee (approval no: EEC/EP/2023/31). DISCUSSION: This study is expected to broaden our understanding of the intricate interactions between the COVID-19 pandemic's impact, resilience, and mental health outcomes. The focus on university students' psychological wellbeing is consistent with the call by the WHO to focus on mental health (World Health Organization, 2019).