Background Motor and emotional variables, plus other factors like gender, influence how preadolescent schoolchildren perceive their motor competence level. Objective By means of a hierarchical linear regression analysis, this longitudinal study aimed to determine the predictive value that coordination, anxiety and self-esteem at the age of 9 years can have on the self-perceived motor competence variable at the age between 11 and 12 years. Methods Data collection was performed with 224 pupils at a first time point with grade-4 Primary Education (PEd) pupils (mean age 9.11±.32 years) and a second time point with grade-6 PEd pupils (11.49±.50 years). Results The results evidenced that coordination, anxiety and self-esteem at the age of 9 years predicted self-perceived motor competence at the age between 11 and 12 years. For the female gender, age explained 5% of the variance for self-perceived motor competence, coordination explained 19% and anxiety 8%. The male gender explained 7% of the variance for self-perception, coordination explained 23% of further variance, anxiety 16% of variance and self-esteem 11%. Conclusions The evidence found reveals the importance of more globally understanding motor competence to promote more suitable and facilitating conditions that you need to perform physical activity at school and elsewhere.