<p>Many children exhibit low levels of movement competence, which is foundational for lifelong physical activity. Preschool years are critical for developing competencies, yet existing interventions lack effectiveness. Ball-based activities offer a promising approach due to their potential to enhance motor skills and promote social interaction. This study evaluated the preliminary effects of the “Ball-Based Play in Preschools” intervention on motor skills in children aged 3–6 years using a stepped-wedge-case-controlled design. Eight preschools participated, with staggered implementation across two arms. Motor skills were assessed using the Movement-ABC-2 test at three timepoints. The intervention emphasized inclusive, play-based ball activities, supported by professional development and collaboration with local sports clubs. Data were analyzed using linear mixed models and complete case analyses. Significant improvements were observed in total motor competence and aim-and-catch skills, increasing by 7.1–10.3 percentile points and 17.2–21.0 points, respectively. No significant changes were found for manual dexterity, and balance showed only marginal improvement. Complete case analyses confirmed a moderate effect size for aim-and-catch skills (<i>d</i> = 0.62), with larger gains among girls (<i>d</i> = 1.01). The intervention shows promise in enhancing general motor competence and ball-related skills. These findings support further development and scaling of the intervention, with a focus on refining components targeting manual dexterity and balance.</p>