Background: During pregnancy, nutritional requirements increase and if not met, pregnancy-related complications may manifest. To prevent these undesirable outcomes, the World Health Organization recommends daily oral iron and folic acid (IFA) supplementation as part of antenatal care. Despite this recommendation, the use of IFA supplements is still very low in several developing countries. Additionally, no prior information exists regarding the level of consumption of IFA in Eswatini. Thus, this study aimed to determine the prevalence of consumption of IFA supplements and to identify factors associated with the consumption of IFA supplements among pregnant women in Eswatini. Methods: A cross-sectional questionnaire survey was conducted among 330 pregnant women aged ≥ 18 years in their third trimester in Eswatini. Participants were recruited from eight purposively selected healthcare facilities from July 2019 to October 2019. Good consumption was defined as consuming all or almost all IFA supplements throughout pregnancy. Results: During the first trimester, 10.3 % of the participants consumed all or almost all IFA supplements. In the second and third trimesters, those who consumed all or almost all supplements were 37 and 39.7 %, respectively, for iron and 37.6 and 40.9 %, respectively, for folic acid. Barriers, including side effects, forgetfulness, safe previous pregnancies without IFA, others’ advice against consumption, IFA stock-outs, inability to meet transport costs, and inadequate supply of IFA tablets, contribute to low consumption of IFA. Multivariate logistic regression models showed that the barriers were inversely associated with good consumption of IFA supplements. Better knowledge and attitude toward IFA and older maternal age were positively associated with good consumption of IFA supplements. Conclusions: Low consumption of IFA supplements in overall pregnancy is mainly owing to the late antenatal care attendance. Strategies such as establishing a preconception care unit and school-based provision of IFA may be helpful. It is evident that most women still lack knowledge, and some have negative attitudes about IFA supplements. Health education to raise awareness and emphasize the importance of starting antenatal care early as well as consuming supplements on time should be revisited and intensified. Multiple strategies such as including community health care workers for distributing IFA supplements, discussing with clients about the measures to reduce forgetfulness, advising ways to prevent and manage the side effects, providing subsidies to cover transport costs, and ensuring adequate supply of IFA supplements in facilities may need to be employed to reduce the identified barriers.