Maternal malnutrition, which has been a problem in Madagascar for several years, has been rising despite interventions to improve the situation. This study aims to identify the socioeconomic determinants of malnutrition among mothers who are one of the most vulnerable groups.A cross sectional study was carried out among 670 mothers aged 18 to 45 living in the Amoron’i Mania region of Madagascar. The study was conducted during the post-harvest period. The nutritional status of mothers was assessed by anthropometry. A Body Mass Index (BMI) lower than 18.5 kg/m2 or an arm circumference lower than 220 mm were used to define malnutrition. Data on the characteristics of the mothers and their households were also collected. Multiple logistic regression was used to identify factors associated with maternal malnutrition.The prevalence of maternal undernutrition is estimated at 17% (95% CI: 14–20) according to BMI and 9% (95% CI: 7–11) for Mid Upper Arm Circumference (MUAC). In the multivariate analysis, using BMI, the factors significantly associated with malnutrition were: the household size equal to or greater than 6 (AOR = 1.59 [1.04–3.42], p = 0.029) and use of unsafe water source (AOR = 1.99 [1.02–3.85], p = 0.030). For the MUAC, the factors associated are: use of unsafe water source (AOR = 2.82 [1.01–7.97], p = 0.041) and increased number of children under five years old (AOR = 1.38 [1.02–1.89], p = 0.025).This study confirmed the importance of mothers’ malnutrition in the study area. Fight against maternal malnutrition needs interventions to improve access to safe drinking water and to promote family planning.