The number of students experiencing mental health problems has risen across Europe in recent years. Besides a detrimental effect on study success, there may be lasting negative consequences. Because mental health problems can arise due to chronic perceived stress, we focus on students’ stress perceptions. Based on two large-scale student surveys in Germany, we investigate stress perceptions during two phases of the COVID-19 pandemic (2020 and 2021), when different restrictions were in place. The empirical results—obtained by estimation of structural equation models—show that academic workload was constantly the main stress factor for students in both years. Financial stress was especially significant during the economic restrictions in 2020, accounting for more than one-third of the impact of academic workload. In addition to personal resources, social contact proved to be a buffer against perceived stress. During the social restrictions in 2020, increased social contact—when possible—significantly reduced perceived stress, lowering it by one-quarter relative to academic stress. The results also show an association between perceived stress, decreased life satisfaction, and a higher risk of dropping out of higher education.