BackgroundUndernutrition during pregnancy is an important public health problem. It is highly prevalent in Ethiopia but not sufficiently addressed yet. Hence, this study aimed to assess the prevalence of undernutrition and its associated factors among pregnant mothers in Konso district, Ethiopia.MethodsCommunity-based cross-sectional study was conducted with a qualitative inquiry from December 2018 to January 2019. A multistage stratified sampling technique was used to select 527 subjects and quantitative data were collected from these subjects using a structured interviewer-administered questionnaire and additionally qualitative data were generated through two focus group discussions among purposely selected discussants. Mid upper arm circumference (MUAC) was measured by standard non-stretchable MUAC tape. Data were entered into Epi-data version3.1 and analyzed by SPSS version 21. In multivariable binary logistic regression, a statistically significant association was declared at p-value < 0.05 while thematic framework analysis was employed for the qualitative data.ResultsAmong 501 participants, the overall prevalence of undernutrition (MUAC < 23 cm) was 43.1% (95% CI 38.7–47.5%). Household food security (AOR = 3.1; 95% CI: 2.1–4.6), low dietary diversity score (AOR = 4.9; 95% CI: 2.6–9.2), medium dietary diversity score (AOR = 2.3; 95% CI: 1.2–4.7), absence of latrine (AOR = 1.8; 95% CI: 1.2–2.6) and having family resource decision making by husband only (AOR = 1.7; 95% CI: 1.1–2.6) were significantly associated factors. Traditional believes to restrict food such as egg, milk, and milk products, avocado for women, weak nutrition education and malnutrition screening program, daily consumption of locally prepared alcoholic drink called “Cheka”, drought-prone nature of this setting, traditional way of farming practices and low socio-economic status were found to be barriers for women’s undernutrition.ConclusionsThe prevalence of undernutrition was found to be higher than previously reported findings. Household food security, dietary diversity, latrine availability, family resource decision making, food restrictions, weak maternal nutrition education, and malnutrition screening program, the practice of depending on a local alcoholic drink called “Cheka”, drought, traditional way of farming and low socio-economic status were identified factors. Hence, interventions targeting maternal nutrition education, hygiene, and sanitation promotion, household food insecurity improvement strategies should be implemented to improve the nutritional status of pregnant women.