The COVID-19 pandemic has had its impact on research and researchers, and hence potentially on the future of academia. Yet, empirical evidence on the impact of COVID-19 on PhD candidates is limited. This study explores the influences of the pandemic on PhD candidates’ progress and wellbeing. In addition, the aim is to identify potentially particularly vulnerable candidate groups. In total, 768 PhD candidates from a Finnish research-intensive multidisciplinary university participated in the mixed method study in spring 2021. The data were collected with the doctoral experience survey. In general, the PhD candidates estimated that the COVID-19 pandemic had hindered their progress and decreased their study wellbeing. The negative impact boiled down to the reduced access to data or participants, erosion of scholarly support networks, reduced access to the institutional resources, poor work–life balance and mental health problems. Results further implied that the international candidates, those studying at the university full-time, engaging in research teams, candidates from natural sciences and those at the mid-phase of their studies employed increased risk of suffering from negative COVID-19 pandemic influences. Results can be used in building well-fitted re-creative actions in supporting the PhD candidates to overcome challenges set by the pandemic.