Abstract: Higher education institutions in Austria switched to emergency distance learning in March 2020 to mitigate the spread of COVID-19. Due to the sudden change, students and instructors scarcely had time to adjust to the new demands. Initial cross-sectional studies pointed to the risks of emergency distance learning for students’ intrinsic motivation, self-regulation, and learning behavior. We investigated the longitudinal effects between the satisfaction of the basic psychological needs (competence, autonomy, and social relatedness), intrinsic motivation, and self-regulated learning, applying a cross-lagged panel model. A sample of N = 3,286 students answered four online questionnaires between April 2020 and July 2021. All measured constructs remained stable during that time span. The satisfaction of the basic needs was cross-sectionally related to intrinsic motivation. We found no cross-lagged effects on intrinsic motivation. Self-regulated learning showed small but significant cross-lagged positive effects on intrinsic motivation at all time points. Implications and future research perspectives are discussed.