Background: Endocrine-disrupting chemicals (EDCs) are environmental pollutants that may impair maternal and fetal health by disrupting hormonal systems, including the thyroid. Both iodine deficiency and excess are associated with thyroid dysfunction and adverse obstetrical outcomes. However, the combined impacts of EDCs and iodine exposure on maternal-fetal thyroid homeostasis remain undetermined. We established the Investigating Birth and Thyroid Outcomes of Maternal-Fetal Environmental Exposures (IBM-E) cohort to prospectively assess the effects of maternal exposures to dietary iodine and EDCs on thyroid function, pregnancy complications, and offspring growth and development. Methods: In this prospective observational study, we aim to enroll 556 pregnant women between 2024 and 2027 at a tertiary hospital in Korea. Maternal blood and urine samples will be collected at six time points, spanning from early pregnancy through 15 months postpartum, with infant samples collected at three time points. EDCs will be quantified using ultra-high performance liquid chromatography-tandem mass spectrometry. Thyroid function and urinary iodine concentration will be measured in both mothers and infants. Results: As of the current interim analyses of 193 mothers and 229 neonates, 15.0% of mothers had thyroid dysfunction and 11.4% developed preeclampsia. Preterm birth occurred in 23.8% of cases, and 16.6% of neonates were small for gestational age. Conclusion The IBM-E cohort is designed to enable the longitudinal assessment of gestational environmental exposures and their potential impacts on maternal and fetal thyroid function, as well as pregnancy and neonatal outcomes. The findings of this study may inform preventive strategies and guide policy development in perinatal environmental health.