The goal of the present study was to analyze the joint role that non-cognitive (motivation and self-esteem) and cognitive (verbal fluency and reasoning) factors play on academic achievement, both as a global score and in relation to specific subjects, such as language and literature and mathematics. We also analyzed the mediating role of cognitive factors. We recruited a sample of 133 primary education students (aged 6–9 years old) (47.6% girls, 52.6% boys), to whom various measures of the above-indicated variables were administered. Several predictive models were tested through a mediational regression analysis. The results indicated the relevance of intrinsic motivation together with self-esteem as predictors of academic achievement mediated by the cognitive abilities verbal fluency and reasoning. These relationships differed depending on the specific subject. We discuss the educational implications of these findings and emphasize, on the one hand, that academic achievement depends on both cognitive and non-cognitive factors and, on the other hand, the malleability of cognitive factors, as they seem to improve based on motivation and self-esteem.