Globally, more than a third of pregnant women are anemic, and progress in its prevention and control is slow. Sri Lanka is a lower-middle-income country with a unique public health infrastructure that provides multiple interventions across the lifecycle for anemia prevention, despite which anemia in pregnancy remains a challenge. Studying the factors associated with maternal anemia in this context would provide unique information on challenges and opportunities encountered as low-and-middle-income countries attempt to control anemia by improving health care coverage. All first-trimester pregnant women registered for antenatal care in the Anuradhapura district between July 2019 to September 2019 were invited to participate in the baseline of a cohort study. Interviewer-administered and self-completed questionnaires were used. Anemia was defined using a full blood count. A hierarchical logistic regression model was built to identify factors associated with anemia. Out of 3127 participants, 451 (14.4%) were anemic. According to the regression model (Chi-square = 139.3, p<0.001, n = 2692), the odds of being anemic increased with the Period of gestation (PoG) (OR = 1.07, 95% CI = 1.01–1.13). While controlling for PoG, age and parity, history of anemia (OR = 3.22, 95%CI = 2.51–4.13), being underweight (OR = 1.64, 95%CI = 1.24–2.18), having the last pregnancy five or more years back (OR = 1.57,95%CI = 1.15–2.15) and having used intrauterine devices for one year or more (OR = 1.63, 95%CI = 1.16–2.30) increased the odds of anemia. Breast feeding during the last year (OR = 0.66, 95%CI = 0.49–0.90) and having used contraceptive injections for one year or more (OR = 0.61,95%CI = 0.45–0.83) reduced the risk of anemia. Proxy indicators of being in frequent contact with the national family health program have a protective effect over the socioeconomic disparities in preventing early pregnancy anemia. Maintaining the continuum of care through the lifecycle, especially through optimizing pre and inter-pregnancy care provision should be the way forward for anemia control.