Background: Congenital malformations are structural, functional, and metabolic defects that develop during the organogenesis period and present at birth or later in life. There has been little research on congenital malformations in Ethiopia, knowledge on the incidence of birth defects at birth is unknown and the etiologies of the anomalies are limited. This study, therefore, aimed to assess the modifiable risks of congenital anomalies among women in Bale zone hospitals, Ethiopia. Methods: An unmatched case-control study was conducted from February 2018 to January 2019 in the Bale zone; namely Goba referral hospital, Robe, Ginnir and Dolomena hospitals. A total of 409 women were selected. Mothers who gave birth with any type of congenital malformation were assigned as cases and those who gave live births without any congenital abnormalities were assigned as controls. Controls were selected by the lottery method from the labor ward. For each case, two consecutive controls were included. Data were entered into Epi-data 3.1 and exported into Statistical Package for the Social Sciences (SPSS) version 21 for analysis. Logistic regression was conducted to analyze the data. Results: Alarmingly, women who had been exposed to pesticides during the current pregnancy were two times more prone to give congenital malformed infants than their counterparts (AOR = 3.19; 95% CI = 1.31, 10.96). Additionally, those women who chewed khat during the periconceptional period were two times more likely to have congenital malformed infants as compared to women who did not engage in this activity (AOR = 2.40; 95% CI = 1.11, 5.19). Conclusions: Urgent attention needs to be given by public health professionals and services to khat chewing and maternal exposure to pesticides during pregnancy to reduce the risk of congenital malformations.