Objective: Motor competence development from early to middle childhood is accompanied by great variance. This course can be influenced by many factors in the ecosystem. The objective of this study was to examine which individual characteristics are associated with an undesirable motor competence development during the transition from early to middle childhood. Methods: A longitudinal study was conducted between February 2020 and May 2022. Actual and perceived motor competence and the potential determinants physical activity enjoyment, weight status, and organized sports participation of children (49% boys) aged 4–6 years old at T0 (N = 721) were measured at two points in time, separated by a two-year interval. Associations between potential determinants and AMC, including interactions with time, were analyzed using linear mixed-effect regression models with continuous motor quotient scores as outcome variables. Results: Overweight, obesity, and lack of organized sports participation were associated with lower motor quotient scores over time. Multivariate analyses showed that associations of weight status (overweight and obesity) and
sports participation with motor quotient scores remained significant after adjustment for variations in perceived motor competence and physical activity enjoyment. Conclusions: Excessive body weight and lack of sports participation from early childhood are associated with an increased risk of an undesirable motor competence development over time.