Background: Chronic energy deficiency (CED) can have serious health consequences in both the mother and the baby. The aim of this study was to determine factors associated with CED in pregnant women. Methods: This cross-sectional study was done on 115 pregnant women referred to two health centers in the Konawe District (Indonesia) in 2021. After determining the prevalence of CED, data on different demographic and socioeconomic characteristics including family income, nutritional status, adherence to Fe tablet consumption and food availability were collected using questionnaires. Relationship between the variables and prevalence of CED was assessed using the Chi-square test at significance of 0.05. Results: The prevalence of CED was 36.5% among pregnant women. The prevalence of CED was significantly associated with family income (P=0.001), nutritional status (P=0.001), adherence to Fe tablet consumption (P=0.007) and food availability (P=0.002). The logistic regression test showed that family income had the strongest association with the prevalence of CED (OR=2.197; 95% CI: 1,248-3.868). Conclusion: The prevalence of CED is higher in pregnant women with low income, poor nutritional status, and limited access to food and poor adherence to Fe tablet consumption. We suggest increasing food security at the family level by providing information to women in preconception stage through counseling, flip charts and posters.