Several population-specific genetic, sociodemographic, and maternal lifestyle factors are related to iron status in early pregnancy, and their identification would allow preventive actions to be taken. The study aimed to identify maternal factors associated with iron deficiency (ID) in early pregnancy in non-anaemic pregnant women from a European Mediterranean country. Cross-sectional study using the initial population of the ECLIPSES study performed in non-anaemic pregnant women before gestational week 12. Serum ferritin (SF) and haemoglobin concentrations were measured to evaluate iron status, and ID was defined as SF < 15 µg/L. Several sociodemographic and lifestyle data were recorded and used as covariates in the multivariate-adjusted regression models. Out of the 791 participants, 13.9% had ID in early pregnancy. Underweight (OR 3.70, 95%CI 1.22, 15.53) and parity (1 child: OR 2.03, 95%CI 1.06, 3.88; ≥ 2 children: OR 6.96, 95%CI 3.09, 15.69) increased the odds of ID, while a high intake of total meat (≥ 108.57 g/day: OR 0.37, 95%CI 0.15, 0.87), red/processed meat (≥ 74.29 g/day: OR 0.70, 95%CI 0.35, 0.98), protein (≥ 65.05 g/day: OR 0.85, 95%CI 0.30, 0.99), and dietary iron (≥ 8.58 mg/day: OR 0.58, 95%CI 0.35, 0.94) protected against it. Smoking was also associated with a reduction in ID odds (OR 0.34, 95%CI 0.12, 0.99). Baseline BMI, parity, smoking, and diet are associated with ID in early pregnancy in non-anaemic women. Pregnancy planning policies should focus on women at higher risk of ID, such as those who are underweight, multiparous, or following vegetarian diets. This clinical trial was registered at www.clinicaltrialsregister.eu as EudraCT number 2012–005,480-28 and at www.clinicaltrials.gov with identification number NCT03196882.