Background Supervisor support is crucial for the successful and timely completion of the PhD and the largest contributor to PhD students’ overall job satisfaction. The COVID-19 pandemic affected PhD students’ life substantially through delayed experiments, missed timelines, running out of funding, change to online team- and supervisor meetings, mandatory working from home, and social confinement. Aim This contribution considers PhD students’ satisfaction scores to reflect the extent to which PhD students felt supported by their supervisor during the COVID-19 pandemic so far and aims to investigate to what extent did PhD students’ satisfaction with supervisor support changed over time. Method It uses two longitudinal two cohorts of wave 4 to 5 of the PhD Survey at a Belgian university. These cohorts are representative of two different ways the COVID-19 pandemic might have impacted doctoral research. Cohort 1 (n = 345) includes a pre-COVID measurement (April-May 2019) and a measurement immediately after the start of the abrupt lockdown in April-May 2020. Cohort 2 (n = 349) includes the measurement at the onset of the pandemic in 2020 and after a year with continuously changing containment policies (April-May 2021). The composite measure of satisfaction with supervisor support is based on six items with high internal consistency. Results No significant net effect of time was revealed. Instead within subject interactions with time showed that in cohort 1, PhD students at the start of their PhD trajectory and PhD students with family responsibilities reported lower supervisor satisfaction scores over time. In cohort 2, PhD students not pursuing academic careers reported lower satisfaction scores over time. Conclusion In times of crises, special attention needs to be paid to PhD students who are extra susceptible to uncertainties because of their junior status or personal situation, and especially those PhD students for whom doctoral research is not a trajectory to position themselves in academia.