Mental health issues among Ph.D. students are prevalent and on the rise, with multiple studies showing that Ph.D. students are more likely to experience symptoms of mental health-related issues than the general population. However, the data is still sparse. This study aims to investigate the mental health of 589 Ph.D. students at a public university in Germany using a mixed quantitative and qualitative approach. We administered a web-based self-report questionnaire to gather data on the mental health status, investigated mental illnesses such as depression and anxiety, and potential areas for improvement of the mental health and well-being of Ph.D. students. Our results revealed that one-third of the participants were above the cut-off for depression and that factors such as perceived stress and self-doubt were prominent predictors of the mental health status of Ph.D. students. Additionally, we found job insecurity and low job satisfaction to be predictors of stress and anxiety. Many participants in our study reported working more than full-time while being employed part-time. Importantly, deficient supervision was found to have a negative effect on Ph.D. students’ mental health. The study’s results are in line with those of earlier investigations of mental health in academia, which likewise reveal significant levels of depression and anxiety among Ph.D. students. Overall, the findings provide a greater knowledge of the underlying reasons and potential interventions required for advancing the mental health problems experienced by Ph.D. students. The results of this research can guide the development of effective strategies to support the mental health of Ph.D. students.