Numerous studies have examined the role of socio-economic status on physical activity, obesity, and cognitive performance in youth or older adults, but few studies have examined the role of neighborhood socio-economic status (NSES) on motor or cognitive performance in kindergarten children. This study aimed to examine whether lower NSES (measured by the social data atlas) was associated with lower motor and inhibitory control performance in kindergarten children. One hundred twenty-nine preschoolers were recruited from eight kindergartens in low and high NSES areas in Stuttgart, one of Germany’s largest metropolitan areas. Motor functioning (Movement Assessment Battery for Children, MABC-2; Manual Dexterity, Aiming and Catching, and Balance) and inhibitory control (Flanker Task, Go/NoGo Task) were assessed in a sample of 3- to 6-year-old children within a cross-sectional study. Children from a low NSES background showed the expected difficulties in inhibitory control and motor performance, as indicated by poorer performance than children from a high NSES background. Sex-specific analysis revealed girls from low NSES areas to have the lowest fine motor control; children with low NSES reach a Developmental Coordination Disorder at-risk status of 13% (boys and girls), in contrast to children with high SES (boys 9.1%, girls 0.0%). Motor performance and inhibitory control correlated positively with regard to the group from a low NSES background. Researchers and practitioners are advised to develop a more nuanced picture of motor and academic achievement in heterogeneous neighborhoods when designing early intervention programs, particularly with regard to sex differences, with the most significant disadvantage to girls with lower NSES.