Despite years of interventions intended to reduce child malnutrition in South Africa, its negative effects, stunting in particular, persist mainly among children under five years old living in under-resourced regions. A cross-sectional study was conducted to determine the prevalence of malnutrition and associated factors among 404 children under age five attending childcare services with their mothers in selected healthcare facilities of Limpopo Province, South Africa. Anthropometry, socio-demographics and obstetric history were collected. Height-for-age, weight-for-age and body mass index-for-age Z-scores were used to determine stunting, underweight and thinness among children, respectively. Logistic regression analyses were performed to generate the factors associated with malnutrition. Stunting (45.3%) was the prevalent form of malnutrition among children under age five, affecting boys (51.7%) more than girls (38.8%) and children aged 12–23 months (62.4%) more than those <11 months old (40.1%), in addition to the overall prevalence of underweight (29.0%) and thinness (12.6%). Boys had increased odds of stunting (adjusted odds ratio, AOR = 2.07, 95% CI: 1.26–3.41, p = 0.004) and underweight (AOR = 2.17, 95% CI: 1.32–3.57, p = 0.002) than girls. Children aged 12–23 months were more likely to be stunted (AOR = 4.79, 95% CI: 2.36–9.75, p ≤ 0.0001) than children aged ≤11 months. Delayed introduction of solid foods increased the odds of stunting (AOR = 5.77, 95% CI: 2.63–12.64, p ≤ 0.0001) and underweight (AOR = 2.05, 95% CI: 1.08–3.89, p = 0.028). Children with normal birth weight were less likely to be thin (AOR = 0.42, 95% CI: 0.19–0.92, p = 0.029) and underweight (AOR = 0.34, 95% CI: 0.17–0.68, p = 0.003) than children who had low birth weight. Children whose mothers had obtained secondary school education (AOR = 0.39, 95% CI: 0.16–0.97, p = 0.044), and Grade 12 or post-Grade 12 education (AOR = 0.32, 95% CI: 0.12–0.83, p = 0.020) were less likely to be stunted than were children of mothers who had only primary school education. Suboptimal complementary feeding predisposed children to stunting and underweight. National nutrition programs should be context-specific to improve the introduction of complementary foods among children, especially in the remote and poor areas.
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