This study aimed to investigate the influence of a structured movement activity program on the motor development of children aged three to five years attending preschool. Participants were 136 preschool students with normative development at three to four years old who lived in the Region of Murcia (Spain). The McCarthy Children's Psychomotricity and Aptitude Scales (MSCA) battery of psychomotor tests was used to evaluate the motor development profiles of preschoolers before and after the intervention. The sample was divided into two groups: an intervention group (28 students) and a comparison group (108 students). A structured 24 week physical education program was used in the intervention group. An experiential program based on free play was used in the comparison group during the same period. Preschoolers in both groups got a significant improvement in the contrast of pre-intervention with post-intervention in limb coordination. Statistically significant differences in the post-intervention measurements between the comparison group and the intervention group on arm and leg coordination were observed, whereby the intervention group presented higher arm coordination values (F1,134 = 14,389, p = 0.000, η2 = 0.097) and higher leg coordination values (F1,134 = 19,281, p = 0.000, η2 = 0.126) than the comparison group. It was pointed out that structured physical activity education is better educational methodology than free play to achieve adequate motor development in preschool children.