Pregnancy increases the demand for essential metal ions to support fetal development, making the maternal metal ion status a critical determinant of perinatal outcomes. This prospective cohort study examined changes in metal ion levels across the three trimesters, evaluated the influence of preexisting metabolic conditions on the metal ion status, and assessed the associations between maternal metal ion levels and perinatal outcomes in 206 pregnant women from the Biochemical and Epigenetic Origin of Overweight and Obesity (OBESO) cohort receiving care at the Instituto Nacional de Perinatología in Mexico City from 2017 to 2020. Six essential metal ions (iron, zinc, copper, calcium, magnesium, and phosphorus) were measured in blood samples using inductively coupled plasma optic emission spectrometry. Significant variations in the metal ion levels were observed across the trimesters, with notable decreases in iron and magnesium and increases in copper as pregnancies progressed. Maternal hypothyroidism was associated with significantly low levels of zinc and magnesium during pregnancy. Regression analyses revealed robust associations between maternal metal ion levels and perinatal outcomes. For instance, declining magnesium levels as pregnancies progressed were positively associated with gestational diabetes (OR: 2.92, p = 0.04; OR: 2.72, p = 0.03). The maternal metal ion status significantly influences perinatal outcomes.