Computer-based simulations are highly effective in supporting students' deep conceptual understanding of scientific ideas. However, in the unprecedented era of the COVID-19 outbreak, students around the world experienced an induced state anxiety, which may have affected their engagement with the learning environments and ultimately their academic outcomes. This crisis underscores the global need to examine the learning processes and identify means of supporting students' engagement under stressful conditions. With this goal in mind, the current study evaluated the impact of COVID-19 induced anxiety on the learning process of 187 undergraduate students by means of computer-based simulation during a quarantine. Findings show that 56% of the students reported experiencing anxiety following the COVID-19 outbreak. A bivariate parametric analysis demonstrated that this COVID-19 induced anxiety had a negative impact on students' engagement. Indirect model analysis revealed that emotional disaffection in terms of boredom mediated the negative effect of COVID-19 induced anxiety on students' engagement. From a theoretical perspective, these findings highlight the pivotal role of boredom in students' learning processes in times of externally induced anxiety. From a pedagogical perspective, our findings highlight the necessity to implement teaching approaches that attend to boredom to mitigate the negative effects of externally induced anxiety.