Background: In Guatemala, the IV National Maternal and Child Health Survey 2014-2015 indicated that about one every two children < 5 years-of-age are stunted (length-height-for-age z-scores<-2). Childcare programs offer a cost-effective opportunity to deliver early education and learning opportunities, health, and nutrition services in a safe environment, especially for children in poverty or suffering from neglect. The purpose of this study was to compare growth outcomes, math performance, fluid intelligence, and receptive vocabulary between 8- year-old children in second grade that attended the Guatemala City Municipal Nurseries (GCMN) and received micronutrient supplements vs. sex, grade, and age-matched children (controls) that did not attend the municipal preschools. Methods: A cross-sectional design nested in a retrospective cohort between 2015-2019 was performed. Both GCMN children and control participants were asked to complete a math-, a receptive language- and a fluid intelligence test. Primary caregivers completed a sociodemographic survey. General and generalized linear mixed effect models were constructed to compare children that attended the GCMN vs. controls prior to elementary school. Models were adjusted by maternal education, sex, asset score, and school, data collection year, and case/control pair were included in the models as random effects. Results: Children that attended the GCMN exhibited greater math and fluid intelligence scores relative to controls in adjusted models [ß = 6.48; 95% CI (2.35–10.61)] and [ß = 1.20; 95% CI (0.12–2.29)], respectively. Lower odds of stunting were significant for children who went to any childcare institution [AOR = 0.28; 95% CI (0.09–0.89)]. Conclusions: Our findings support the effectiveness of integrating high-quality early nutrition and education via childcare programs serving low-resourced populations, in child’s nutritional status and academic performance. This model may be scalable and prove effective in improving children wellbeing from impoverished backgrounds.