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COVID-19 has impacted children’s mental health (CMH). Person-centred research on MH outcomes of COVID-19 on disadvantaged children based on a subset of risk (and protective) factors is limited. This mixed-methods study used a naturalistic experiment design to investigate profiles of CMH transitions following the onset of COVID-19 in 297 low-income children in Toronto. Latent transition analysis revealed nine transition profiles, further grouped by stability, improvements, and decline in CMH. Crosstabulation was used to examine what sociodemographic and maternal factors (i.e., parenting and maternal mental health) are related to these transition profiles. We discuss the policy and practical implications of understanding the subtleties of CMH changes during large-scale adversities situations and the impact of maternal factors.