Anemia in pregnancy is a major public health problem, especially in developing countries. The most common cause is nutritional deficiencies, especially iron deficiency. Adequate nutritional intake from food is essential during pregnancy. Therefore, this study aimed to investigate the relationship between food access and intake patterns with the incidence of iron deficiency among pregnant women living in the slum settlement in Makassar City. This research is a sub-study of the Indonesian Birth Cohort Study based in Makassar City. This sub-study used a cross-sectional design and recruited 173 pregnant women in their second and third trimesters using total sampling. All data were collected using a structured questionnaire and recorded using KoboToolbox software. Serum ferritin levels were examined for iron status using the ELISA method at the Microbiology Laboratory Unit at Hasanuddin University Teaching Hospital. The statistical data were analyzed using STATA version 14 with Chi-square analysis and logistic regression. The prevalence of iron deficiency in pregnant women living in slum settlements in Makassar City was 78%. Logistic regression analysis showed that inadequate food diversity (AOR: 2.58; 95% CI: 1.17-5.69; P = 0.019) and food taboos (AOR: 2.81; 95% CI: 1.26-6.26; P = 0.011) were significantly associated with the incidence. Most pregnant women living in slum settlements in Makassar City experienced iron deficiency. Pregnant women who experience iron shortages have been connected to food taboos and dietary diversity.