Iron deficiency anaemia during pregnancy is a common public health problem that negatively affects maternal and newborn health. This study aims to identify the rate of maternal compliance with the recommended iron and folic acid (IFA) supplementation during pregnancy and to identify factors associated with maternal compliance and non-compliance. A hospital-based cross-sectional study was conducted among 703 women at 0–4 days postpartum. The prevalence of anaemia at the initial antenatal clinic (ANC) visit and at the third trimester were 20.8% and 44.9%, respectively. The rate of IFA supplementation compliance during pregnancy was 80.1%. Forgetfulness (66.9%) was the major reason for non-compliance, followed by side effects (15.7%). Maternal employment [OR (95%CI): 1.7 (1.00–2.89)], history of a low birth weight infant [OR (95%CI): 0.4 (0.19–0.9)] and history of anaemia [OR (95%CI): 0.4 (0.12–0.98] were significantly associated with maternal compliance with IFA supplementation. Only 26.6% of the participants adhered to dietary recommendations during the period when IFA supplements were provided. The rate of maternal compliance with IFA supplementation was high. However, the prevalence of maternal anaemia during pregnancy was also high, which was presumably due to poor dietary compliance despite high IFA supplementation compliance.