In Malawi, the prevalence of intimate partner violence (IPV), or closely related violence, is estimated at 42% according to the 2015–16 Malawi Demography and Health Survey (MDHS). This study investigated the association between women’s autonomy in household decision-making participation as well as sexual autonomy and IPV among married and cohabiting women aged 15–49 years in Malawi. Secondary data were taken from the 2015–16 MDHS. Multivariate analysis was performed using a stepwise forward logistic (binary) regression model to assess the association of dimensions of women’s autonomy in the household and selected control variables with IPV. No association was found between dimensions of women’s autonomy in the household and IPV. However, other variables did have an association with some form of IPV, namely women justifying wife beating, having a jealous partner, being accused of unfaithfulness by their partner, having a partner who drinks alcohol and having a partner with another woman or more. In addition, religion, ethnicity, women education level and women’s occupation were found to be associated with the risk of experiencing IPV. The study recommends policy interventions aimed at supporting youth, especially girls, to complete secondary education before they marry or cohabit; the development of accessible and affordable psycho-social counselling specialists and platforms for married and cohabiting couples; nationwide rigorous advocacy and civic education on IPV; and enforcement of Malawi’s 2006 domestic violence law.