Summary Early-on in the COVID-19 pandemic when universities were closed as part of the nation-wide public health response to the COVID-19 outbreak, studying and student life significantly changed. Based on limited evidence the aim of this study was to explore the relationship between sense of coherence (SoC), future worries and mental health outcomes among German university students during the early phase of the pandemic. A cross-sectional online survey with n = 14 916 participants was carried out by inviting all private and public universities in Germany. All data were analysed using univariate, bivariate and multivariate statistics. Findings indicate a low and very low wellbeing for 38% of university students. Moreover, 29% reported being affected by at least two health complaints more than once week. Both health outcomes follow a social gradient and could be more frequently observed for respondents with lower subjective social status and female students. Regression analysis revealed significant association between the SoC dimensions and wellbeing (OR: 1.2−2.03) as well as health complaints (OR: 1.58−1.71). A high level of future worries was associated with low/very low wellbeing (OR: 2.83) and multiple health complaints (OR: 2.84). Based on the results, the public health response to the pandemic and university health promotion should therefore consider student mental health as an important target within their policy and action frameworks.