Background Intimate partner violence (IPV) against women is a major public health concern in low income countries. Violence against pregnant women has adverse effects on maternal and newborn outcomes. This study aimed to assess the prevalence and associated factors of intimate partner violence in Southeast Ethiopia pregnant women. Methods Institutional based cross-sectional study was conducted on pregnant women who were attending antenatal care (ANC) in Bale Zone health institution during study period. Face to face interviews were conducted using a pre-tested structured questionnaire. Data related to socio-demographic characteristic, pregnancy and reproductive history, intimate partner behavior and IPV encountered during recent pregnancy was gathered for this study. Descriptive analysis and logistic regression were used for the data analysis. Odds ratio with 95% CI was computed to determine the presence and strength of associated factors with IPV. Results A total of 612 pregnant women participated in the study. Of these, 361 (59.0%) pregnant women faced at least one type of IPV during the recent pregnancy. Physical violence (20.3%), sexual violence (36.3%), psychological/emotional violence (33.0), controlling behavior violence (30.4%) and economic violence (27.0) were the type of IPV encountered by participants. An intimate partners who were drank alcohol [AOR = 2.9; 95% CI: (1.5–5.4)], partners who were chewed Khat [AOR = 1.7; 95% CI: (1.1–2.6)], partners who were smoked cigarette [AOR = 2.6; 95% CI: (1.4–4.9)], partners who had aggressive behavior [AOR = 2.8; 95% CI: (1.7–4.6)], having partner age ≥30 year old [AOR = 1.8; 95% CI: (1.2–2.9)], unwanted pregnancy [AOR = 3.3; 95% CI: (1.9–5.5)] and history of adverse pregnancy outcome [AOR = 2.1; 95% CI: (1.2–3.6)] that were the factors that significantly associated with IPV of the pregnant women. Conclusion The prevalence of IPV during pregnancy was high among the study participants. Intimate partners’ use of substance, intimate partners’ aggressive behavior, older intimate partners, unwanted pregnancy and history of adverse birth outcome were identified as associated factors for IPV. IPV needs to be considered during ANC service and integrated into the sexual and reproductive health education. Community-based interventions should be advocated as a way of health promotion. Counseling, awareness creation, service provision and program design on IPV is mandatory to minimize the victim.