Abstract Background Nursing is a challenging profession that demands quick adaptation to changing conditions. The COVID-19 pandemic has placed unprecedented pressure on nursing teams, leading to high-stress levels and uncertainty. This study examines how nurses’ emotional response at the start of the pandemic predicts their trust in the healthcare system and pandemic fatigue after three morbidity waves. Methods This study included collecting self-reported data among Israeli nurses in three time periods: 346 nurses during March-May 2020 (T1), 260 nurses during June-July 2020 (T2), and 91 nurses during February 2022 (T3). Change in the study variables was assessed using repeated-measure ANOVA. Two multiple linear regression models were calculated for trust and pandemic fatigue at T3, with the emotions at T1 and professional seniority as predictors. Results A significant increase in negative emotions was observed between T1 and T2 (M = 2.65, SD = 1.12 and M = 3.20, SD = 1.29 respectively). Furthermore, there was a significant decrease in trust levels between T1 and T3 (M = 4.68, SD = 1.14 and M = 4.07, SD = 1.08 respectively). The regression model for trust was significant, with 20% of the variance explained in it, revealing that higher positive emotions at T1 predicted higher trust at T3. Similarly, the regression model for pandemic fatigue was significant (R2=22%), showing that lower professional seniority and lower positive emotions at T1 were predictors of higher pandemic fatigue at T3. Conclusions During a crisis, nurses may experience intense negative emotions like fear and anxiety. However, positive emotions, such as pride and a sense of mission, are crucial in maintaining their trust and preventing the onset of pandemic fatigue. Healthcare organizations should promote emotional support and provide emotional resources so that nurses can continue to deliver high-quality care even during challenging times. Key messages • During times of crisis, it’s crucial to foster positivity and encourage a sense of pride and accomplishment in nursing staff. • Healthcare organizations must provide emotional support to nursing teams in routine and crisis situations to prevent burnout and maintain trust and long-term functioning.