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Academia has been facing a mental health crisis particularly affecting early career researchers (ECRs). Moreover, the COVID-19 pandemic posed an unprecedented burden on the mental health of many individuals. Therefore, we cross-sectionally investigated how doctoral researchers (N = 222) evaluate their mental health status and satisfaction with their PhD training before and during the pandemic. As compared to self-reported, retrospective evaluations about the pre-pandemic state, we found decreased satisfaction with PhD training and overall well-being. The whole sample exhibited high levels of personal and work-related burnout, a fifth indicated clinically meaningful levels of depressive symptoms and almost 25% experienced severe loneliness. When exploring predictors of depression, anxiety, and burnout, we identified low satisfaction with PhD training as the most prominent predictor for poor mental health, suggesting a link between the doctoral work and their mental health status. Females vs. males and doctoral researchers in individual doctorate vs. structured PhD programs reported higher symptoms of burnout. Our study replicates previous findings of poor mental health in doctoral researchers and indicates further decreases of mental wellbeing under the influence of the pandemic. Systematic adjustments in academia are required to improve the mental health of ECRs.