Objective: To investigate perceived changes in academic self-efficacy associated with self-reported symptoms of COVID-19, changes in mental health, and trust in universities management of the pandemic and transition to remote education during lockdown of Swedish universities in the spring of 2020. Methods: 4495 participated and 3638 responded to self-efficacy questions. Associations were investigated using multinomial regression. Results: Most students reported self-experienced effects on self-efficacy. Lowered self-efficacy was associated with symptoms of contagion, perceived worsening of mental health and low trust in universities capacity to successfully manage the lockdown and transition to emergency remote education. Increased self-efficacy was associated with better perceived mental health and high trust in universities. Conclusion: The initial phase of the pandemic was associated with a larger proportion of students reporting self-experienced negative effects on academic self-efficacy. Since self-efficacy is a predictor of academic performance, it is likely that students academic performance will be adversely affected.