In response to the Coronavirus Disease 2019 (COVID-19) pandemic, various measures were taken to contain its spread, including restrictions on physical education and sports clubs. These measures substantially limited children's physical activity behaviors and may have compromised their motor development. Such compromising effects may be particularly prevalent among children from lower socioeconomic background (SEB) who tend to be less physically active than higher SEB peers. In this study, the impact of COVID-19 pandemic-related restrictions on children's motor development was investigated with respect to children's SEB within the PESCov DFG project. Data from 68,996 children from a metropolitan region in Germany (Age: 8.83 years +- 0.56, range: 6.4–13 years, 35,270 female, 51.1%) assessed between 2011/2012 and 2022/2023 were analyzed as part of the longitudinal cohort study “Berlin hat Talent”. Assessment took place before and after the onset of the pandemic using the German Motor Fitness Test. The test includes assessments of various motor skills covering endurance, strength, coordination, and flexibility. Demographic variables (e.g., age, gender) were collected via questionnaires. SEB was derived on school level, which was determined using the official school type classifications of the state of Berlin. Cross-classified linear mixed effect models were fitted to account for hierarchies in the data, with individual test values (level 1) being nested in motor domains (level 2a) and in participants (level 2b) and participants being nested in schools (level 3b). Outcome measure was motor skill performance transformed from German reference percentiles to z-scores per motor skill. The effects of Time (pre, post LD I, post LD II), Motor Domain, and SEB (continuous, -2–2) were estimated while controlling for Age, Gender, and Secular Trends. Main effects of Time, Motor Domain, and SEB were significant. Further, a significant Time x Motor Domain interaction revealed that motor skills differentially developed during the pandemic. Coordination, strength, and flexibility decreased, while endurance increased. SEB had a negative effect on overall motor development of third graders. However, this effect varied between motor domains (coordination = endurance > strength > flexibility). Totally, motor skills were on average about 4 percentile points lower after lockdown I, and the effect of the pandemic was stronger after controlling for domain-specific secular trends. Results suggest highly differential effects of the pandemic on children's motor development, which should be considered when recovering motor skills in the post-pandemic era. To avert these trends and the lifelong consequences of impaired motor development in childhood, comprehensive monitoring of children’s motor performance levels is needed as well as support programs for children with compromised motor performance, particularly for children from lower SEBs.