BackgroundThe use of 12-h shifts for nursing staff has become common in many healthcare settings, including tertiary hospitals, due to its potential benefits such as reduced handover time and increased continuity of care. However, there is limited research on the experiences of nurses working 12-h shifts, particularly in the context of Qatar, where the healthcare system and nursing workforce may have unique characteristics and challenges. This study aimed to explore the experiences of nurses working 12-h shifts in a tertiary hospital in Qatar, including their perceptions of physical health, fatigue, stress, job satisfaction, service quality, and patient safety.MethodsA mixed method study design was applied consisting of a survey and semi-structured interviews. Data was collected from 350 nurses through an online survey and from 11 nurses through semi-structured interviews. Data was analyzed using Shapiro–Wilk test and the difference between demographic variables and scores were examined using Whitney U test and Kruskal- Wallis test. Thematic analysis was used for qualitative interviews.ResultsThe results from quantitative study revealed nurses perception in working 12-h shift has negative impact in their wellbeing, satisfaction as well as patient care outcomes. Thematic analysis revealed real stress and burnout and experienced an enormous amount of pressure going for work.ConclusionsOur study provides an understanding of the nurse’s experience working 12-h shift in a tertiary level hospital in Qatar. A mixed method approach informed us that, nurses are not satisfied with the 12-h shift and interviews revealed high level of stress and burnout among nurses resulting in job dissatisfaction and negative health concerns. Nurses also reported that it is challenging to stay productive and focused throughout their new shift pattern.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12912-023-01371-0.