During the COVID-19 pandemic, physical inactivity and being overweight increased in children, especially those from lower socioeconomic backgrounds. Additionally, a decrease in motor performance has been increasingly reported; however, there is a lack of meaningful data on the relationship between these findings and socioeconomic status. Therefore, we examined the BMI, BMI z score, the prevalence of overweight/obesity, and motor performance (based on lateral jumping, the standing long jump, and the 6-min run) among three cohorts from timelines before (2016) and during the pandemic (2020, 2021), using a cohort sequential design. Our analysis revealed that all parameters examined showed a significant negative trend over time. For children with a low social burden, the trend was statistically detectable only for lateral jumping and the 6-min run. For children with a high social burden, the prevalence of overweight/obesity increased from 4.2% to 5.4% between 2016 and 2021. The prevalence of being underweight also increased from 3.4% to 4.3% during this time. Motor performance decreased from 11.3% to 12.3%, except in the standing long jump. Children with a high social burden showed significantly lower results (7.4% to 9.6%). Thus, our data confirm an increase in both measurements of overweight/obesity and underweight, as well as a decrease in motor performance under the pandemic conditions, especially in children from socioeconomically deprived backgrounds. These findings affirm the urgent need for action regarding health promotion measures, especially for children with high social burdens.