Multiple caregiving arrangements have become common for childcare globally, and South Africa is no exception. Previous childcare studies mainly focused on the caregiver and household characteristics. Evidence on the influence of childcare on malnutrition is sparse. This study aimed to examine the relationship between exposure to secondary and multiple forms of care and child malnutrition, with a particular focus on child stunting and overweight among children. A cross-sectional study of a sample of 2966 dyads of mothers and children under five were analysed from the 2017 National Income Dynamics Study (NIDS) Wave 5. Descriptive and inferential statistics were used to analyse the data. The results indicated that 22.16% of the children were stunted and that 16.40% were overweight. Most children were mainly cared for at home (67.16%) during the day. Some results of the obtained multivariable analyses show that lack of being cared for in a crèche or school during the day was significantly associated with stunting (odds ratio (OR) 2; confidence interval (CI) 1.10–3.62, p < 0.05) and overweight (OR) 3.82; (CI) 1.60–9.08, p < 0.05). Furthermore, in this study, 69.88% of children who were cared for at home by the primary caregiver had no other forms of multiple care arrangements. The results showing high stunting and overweight rates among children cared for at home suggest that the government needs to look into supporting caregiver parenting. The high unemployment rates in the country highlight the importance of socioeconomic status in childcare and its implication for children’s nutritional outcomes. The study’s findings suggest the need for innovative strategies to address the challenges associated with multi-caregiving which negatively affects children’s nutritional outcomes.