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Studies show an enhanced increase in children’s weight and body mass index (BMI) during the COVID-19 pandemic, and therefore measures to maintain children´s health are of vital importance. This study examines the effects of a 15-week web-based intervention of nutritional education and physical activity on children’s BMI z-score during the COVID-19 pandemic in Vienna. This pilot study was conducted in a Viennese primary school from February to June 2021. The study population included an intervention group and a control group comprising 125 8- to 11-year-olds. The intervention group received online nutritional and physical activity training, whereas the control group received no intervention. Anthropometric measurements were performed before and after intervention for both groups. At baseline, 41.2% were overweight/obese. After the study period, the BMI z-score decreased by 0.06 (±0.21) in the intervention group, whereas it increased by 0.17 (±0.34) in the control group (p<0.001). Further results show that the decrease in BMI z-score according to sex was significant in the intervention group for boys (p=0.004) and girls (p=0.012). In conclusion, an online intervention with combined nutritional education and physical activity training could be an adequate tool to lessen the enhanced increase in body weight during a pandemic. Therefore, further studies and the rapid implementation of such intervention programs are needed.