Understanding the implications of the COVID-19 pandemic on the current generation of youth is critical for post-pandemic recovery planning. This study aimed to identify the most salient child (i.e., connectedness to caregivers, screen time, sleep, physical activity, peer relationships, and recreational activities) and family (i.e., COVID-19 financial impact, maternal depression and anxiety) factors associated with children’s mental health and well-being during the COVID-19 pandemic, after controlling for pre-pandemic mental health. This study included 846 mother–child dyads (child age 9–11) from the All Our Families cohort. Mothers reported on the child’s pre-pandemic mental health at age 8 (2017–2019) and during COVID-19 (May–July 2020), the family’s financial impact due to COVID-19, and maternal depression and anxiety. During COVID-19 (July–August 2020), children reported on their screen time, sleep, physical activity, peer and family relationships, and recreational activities, as well as their happiness, anxiety and depression. After controlling for pre-pandemic anxiety, connectedness to caregivers (
B
− 0.16; 95% CI − 0.22 to − 0.09), child sleep (
B
− 0.11; 95% CI − 0.19 to − 0.04), and child screen time (
B
0.11; 95% CI 0.04–0.17) predicted child COVID-19 anxiety symptoms. After controlling for pre-pandemic depression, connectedness to caregivers (
B
− 0.26; 95% CI − 0.32 to − 0.21) and screen time (
B
0.09; 95% CI 0.02–0.16) predicted child COVID-19 depressive symptoms. After controlling for covariates, connectedness to caregivers (
B
0.36; 95% CI 0.28–0.39) predicted child COVID-19 happiness. Fostering parent–child connections and promoting healthy device and sleep habits are critical modifiable factors that warrant attention in post-pandemic mental health recovery planning.