In higher education, students' trust in the university management may affect both mental health and academic self-efficacy. This longitudinal study, conducted during the most challenging course of the COVID-19 pandemic, uses multinomial regression and causal inference to estimate the effects of students' trust in their universities' strategies for managing the pandemic, on students' self-reported changes in mental health and academic self-efficacy. The analyzed sample (N = 2796) was recruited through online advertising and responded to a baseline online survey in the late spring of 2020, with two follow-up surveys five and ten months later. Results show that positive trust in university management of the pandemic protected against experiencing one's mental health and academic self-efficacy as worse rather than unchanged, both five and ten months after the baseline assessment. The findings emphasize the importance of developing and maintaining trust-building measures between academia and students to support students' mental health and academic self-efficacy in times of uncertainty.