Recent studies highlight the effect of cognitive factors on academic achievement, ignoring motivational, emotional, and social factors. This provides the background for the present study, a meta-analysis on the relationship between academic achievement and motivational factors (motivation, self-concept, and self-esteem), emotional factors (emotional intelligence, emotional competence, and emotional well-being), and social factors (social intelligence, social competence, and social skills) in children aged 6–12 years (37 samples, n = 15,777). The methodology based on the PRISMA protocols was applied: phases of inclusion and exclusion of articles, analysis of effect size, heterogeneity, publication bias, and, finally, meta-regressions and moderation analysis. The results showed a moderate positive effect size (0.321) for motivational and social factors (0.210) and a small positive effect size (0.172) for emotional factors. The moderating effects of age (65% on social factors) and geographical area (52% on motivational factors, 17% on emotional factors, and 76% on social factors) were studied. These results highlight the importance of motivational and social factors regarding academic achievement. In addition, along with the moderating effect of age, that of geographical area emerges strongly given the diversity of contexts studied. Our results highlight the importance that these factors have on academic performance and, therefore, the need to design school plans that address the correct development of these variables.