Abundant studies have examined mental health in the early periods of the COVID-19 pandemic. However, empirical work examining the mental health impact of the pandemic’s subsequent phases remains limited. In the present study, we investigated how mental vulnerability and resilience evolved over the various phases of the pandemic in 2020 and 2021 in Germany. Data were collected (n = 3522) across seven measurement occasions using validated and self-generated measures of vulnerability and resilience. We found evidence for an immediate increase in vulnerability during the first lockdown in Germany, a trend towards recovery when lockdown measures were eased, and an increase in vulnerability with each passing month of the second lockdown. Four different latent trajectories of resilience–vulnerability emerged, with the majority of participants displaying a rather resilient trajectory, but nearly 30% of the sample fell into the more vulnerable groups. Females, younger individuals, those with a history of psychiatric disorders, lower income groups, and those with high trait vulnerability and low trait social belonging were more likely to exhibit trajectories associated with poorer mental well-being. Our findings indicate that resilience–vulnerability responses in Germany during the COVID-19 pandemic may have been more complex than previously thought, identifying risk groups that could benefit from greater support.