Iodine is an essential micronutrient for cognitive development and growth. Optimal intakes are critical during pregnancy. We report the iodine status and thyroid function of pregnant women living in areas previously affected by severe iodine deficiency and in longstanding iodine sufficient areas in Java, Indonesia. This cross-sectional study was conducted in Magelang, Java, from July to November 2015, in four sub-districts; two previously affected by severe iodine deficiency (area 1) and two that were iodine-sufficient (area 2). Iodine intake was estimated using median urinary iodine concentration in spot samples and mean urinary iodine excretion in 3 x 24-hour samples, thyroid hormones (thyroid-stimulating hormone and free thyroxine) were measured in venous blood samples, and iodine content of household salt samples was estimated by titration. We recruited a total of 244 pregnant women, 123 in area 1 and 121 in area 2. Urinary iodine results suggested adequate habitual iodine intakes in both areas (median urinary iodine concentration in area 1: 222 μg/l (interquartile range 189, 276 μg/l), area 2: 264 μg/l (interquartile range 172, 284 μg/l), however, the risk of inadequate intakes increased with advancing trimester (Odds Ratio = 2.59 (95% CI 1.19-5.67) and 3.85 (95% CI 1.64-9.02) at second and third trimesters, respectively). Estimated prevalence of thyroid function disorders was generally low. Salt was iodized to approximately 40 ppm and foods rich in native iodine did not contribute significantly to dietary intakes. Adequately iodized salt continues to prevent iodine insufficiency in pregnant women living in areas previously affected by severe iodine deficiency in Java, Indonesia. Monitoring and surveillance, particularly in vulnerable groups, should be emphasized to ensure iodine sufficiency prevails.