Background The medium-term impact of the COVID-19 pandemic on the wellbeing of children and adolescents remains unclear. More than two years into the pandemic, we aimed to quantify the frequency and determinants of having been severely impacted by the COVID-19 pandemic and estimate its impact on health-related quality of life (HRQoL) and mental health. Methods Data was drawn from a population-based cohort of children and adolescents, recruited between December 2021 and June 2022, in Geneva, Switzerland. We measured the impact of the pandemic via the Coronavirus impact scale, which assesses the multidimensional impact of the pandemic at the child and family level through parent's report. A score higher than one standard deviation above the mean was deemed a severe impact. Parents additionally reported about their offspring HRQoL and mental health with validated scales. Determinants of having been severely impacted were assessed with logistic models, as were the associations between having experienced a severe impact and poor HRQoL or mental health. Results Out of 2101 participants aged 2-17, 12.7% had experienced a severe pandemic impact. Having a lasting health condition, a pandemic-related worsening of lifestyle habits or an unfavorable family environment were associated with having been severely impacted by the pandemic. Participants who had experienced a severe pandemic impact were more likely to present poor HRQoL (aOR=3.1; 95%CI: 2.3-4.4) and poor mental health (aOR=3.9; 95%CI: 2.5-6.2). Conclusions The COVID-19 pandemic may have persistent consequences on the wellbeing of children and adolescents, especially among those with health and family vulnerabilities.