The current study presents a 1-year follow-up investigation of the development of executive functions (i.e., inhibition, updating, and shifting) in children with motor coordination impairments. Cognitive and motor coordination skills of children (N = 94) aged between 5 and 7 years with and without motor coordination impairments were compared. A second focus of the study was on pre-academic skills. The results indicate marked stability of motor coordination impairments and persistent executive functioning deficits in motor-impaired children. Inhibition and shifting performance was consistently lower, compared to the children without motor coordination impairments. Moreover, children with motor coordination impairments showed lower pre-academic skills, facing a substantial disadvantage at the beginning of formal schooling. The combined cognitive and motor problems may be the result of an underlying inhibition deficit or a general automation deficit. Implications for intervention are discussed.