The aim of the study was to evaluate the effects of a structured coordinative exercise intervention based on motor skill elements on physical fitness (PF), motor competence (MC) and inhibitory control (IC) in preschool children. A total of 41 kindergarten children (27 boys and 17 girls) aged between 5 and 6 years participated and were divided into exercise (EG; n = 18) and control (CG; n = 23) groups. The exercise group participated in a structured coordinative exercise programme focusing on locomotor and balance skills such as side-stepping, galloping, jumping and running for 30 min, 2 days a week for 8 weeks. The control group followed the normal curriculum. Children participated in measurements before and after 8 weeks, respectively; motor competence was assessed using the Körperkoordinationstest für Kinder (KTK3+) test battery, which includes eye-hand coordination and other coordinative skills. Physical fitness was measured by balance, agility and vertical jump tests. Inhibitory control was assessed using the Go/NoGo test in the Early Years Toolbox. As a result of the two-factor analysis of variance for mixed measures to determine whether being in the exercising group had a significant effect on the test scores, group by time interaction effect showed that the increase in the scores of the exercise group was significantly higher than that of the control group in the parameters of static balance, KTK sideways jump and KTK eye-hand coordination [respectively: F = 6.993, p = 0.012; 6.443, p = 0.015; 8.180, p = 0.007). The results show that structured coordinative exercises improve PF and MC but have no significant effect on IC. This study targets the development of motor and cognitive skills considered to be important in preschool children and is one of the few studies to evaluate these parameters simultaneously. It also provides a comprehensive perspective on interventions aimed to positively affect health and development in early childhood.Trial Registration: NCT06631248. Registered on October 07, 2024.