This paper reports on changes in the social-emotional well-being of 6- to 12-year-old children tested before the COVID-19 pandemic and during 2020 and 2021. Well-being was assessed using a video game that empowers children to report their own well-being, including school attachment, social and emotional well-being, behavioural conformity and family support. We compared well-being over time for two groups of children in government schools in Queensland, Western Australia and Tasmania. The treatment group of 580 children were tested in 2019 (Time 1) and a second time in mid-late 2020 and early 2021 (Time 2). The comparison group of 841 children were tested twice before the pandemic. Results showed that children in the treatment group reported significantly lower family support at Time 2 than those in the comparison group. This reduction in perceived family support was stronger for girls. In addition, children in the treatment group who reported lower levels of family support at Time 1 reported a steeper decline in family support by Time 2. Finally, boys in the treatment group reported significantly better behavioural conformity and emotional well-being relative to girls over time. Results highlight the varied impacts of the pandemic lockdowns and the need to provide continued support to vulnerable families.