Women’s empowerment is often defined to include aspects of agency, autonomy and choice, which in turn has consequences for facing intimate partner violence (IPV) and the ability of a woman to fulfil childcare responsibilities. This suggests that empowerment is directly and indirectly (via IPV) associated with child nutrition outcomes (CNOs), especially in South Asian countries where gendered norms may place the onus of childcare on mothers. We explore the interplay between empowerment, IPV and CNOs using nationally representative datasets from three South Asian countries—India, Nepal and Pakistan. We use a multivariate probit approach to investigate the direct and indirect effect of women’s empowerment and autonomy on child malnourishment (stunting, wasting and underweight). Across all countries, we find a strong statistically significant effect of improvements in decision-making power on increased likelihood of facing certain types of IPV. We also find a strong negative relationship between facing less severe violence in particular and CNOs across all countries, indicating that such violence experienced by mothers was detrimental to CNOs. Increasing women’s decision-making power within the household can help ameliorate adverse CNOs, and in India particularly, this increase in decision-making autonomy reduced the incidence of stunting and underweight children. The study concludes with limitations and directions for future work.