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We investigated changes in primary schoolchildren's perceptions of the school climate amidst the COVID-19 pandemic and online learning shift. Data from the Modified-Delaware School Climate Survey-Student collected before (Time 1 (T1): October/November 2019) and during the pandemic's initial wave (Time 2 (T2): 12 months later) in Spain, Norway and Poland were analysed. In this repeat cross-sectional pre-post quasi-experimental study, we included a total of 1167 participants at T1 and 1209 participants at T2, ranging in age from 8 to 16 years and representing schoolchildren from fourth to last primary grades. Findings revealed a significant decline (overall OR = 0.80) in school climate perception across dimensions and countries during the pandemic's onset. Boys exhibited more negative perceptions than girls, particularly pronounced in Norway (OR = 0.59). Age also played a role, with a decline as students advanced in age, especially prominent in Poland (overall OR = 0.74). Our results emphasize the necessity of considering gender and age distinctions to enhance school climate during crises and proactively mitigate adverse effects on school climate.