Purpose: During the COVID-19 pandemic, a significant number of measures were taken worldwide to limit the transmission of SARS-CoV-2, and in many ways, changed human life. All these measures had harmful consequences and impacted the well-being of many people. Children were one of the most vulnerable groups. We conducted the present study to assess children’s and staff’s well-being in French-speaking primary schools in Belgium during the COVID-19 pandemic. Methods: A 37-question questionnaire for each child based on the Revised Children’s Manifest Anxiety Scale (RCMAS), and a 14-question questionnaire for each staff based on the Hospital Anxiety and Depression (HAD) scale was undertaken in order to assess the well-being. Multiple logistic regressions were performed to assess the relationship between RCMAS or HAD and other explanatory variables. Staff reported their perception of their current life and their future life in 5 years on a Visual Analogue Scale (VAS). Results: A total of 231 children and 221 staff in 11 primary schools answered the well-being questionnaire between January and May 2021. 53% (122/231) of children had symptoms of anxiety. Girls reported more anxiety symptoms than boys (≥10: 59%; Adj OR = 2.25; 95% CI [1.28; 4.03]). 52% (120/231) of children had a definite state of social desirability. According to age,the youngest (6 - 7 years) children were more likely to have social desirability (≥5: 71%; Adj OR = 3.44; 95% CI [1.53; 8.09]) compared to the oldest (10 - 12 years). Children who did not practice outdoor/street activities were more likely to have social desirability (≥5: 60%; Adj OR = 2.59; 95% CI [1.38; 4.99]). In schools with a higher local incidence of SARS-CoV-2, children were more likely to have social desirability (≥5: 64%; Adj OR = 2.15; 95% CI [1.13; 4.17]). In schools with a lower socioeconomic status, children were more likely to have social desirability (≥5: 72%; Adj OR = 2.74; 95% CI [1.23; 6.37]). Higher RCMAS anxiety (r = −0.18; p < 0.05), physiological ...