Metabolic bariatric surgery (MBS) helps reduce comorbidities, such as hypertension and gestational diabetes, and is more effective than diet management for women with obesity-related health issues. Vitamin B12, vitamin D, and iron play important roles in ensuring the health of a neonate. However, pregnancies occurring after MBS may face complications related to micronutrient deficiencies, particularly of vitamins B12 and D and iron. This study aimed to investigate the vitamin B12, vitamin D, ferritin, and iron status of pregnant women who underwent MBS compared with women without MBS history. The study included 217 pregnant women (105 with a history of MBS and 112 without a history of MBS) who visited a major maternity hospital in Abu Dhabi, United Arab Emirates (UAE) between July 2021 and November 2022. The maternal vitamin B12, vitamin D, iron, and ferritin levels were measured twice, initially during the first or second trimester and subsequently during the third trimester. The iron was measured once during the pregnancy. Vitamin B12 deficiency was higher among pregnant women with MBS history compared to non-bariatric pregnant women (24.4% vs. 3.9%, p < 0.001). Women with a history of MBS had a higher prevalence of vitamin D deficiency (62.3% vs. 37.7%, p < 0.002). Linear regression analysis indicated that vitamin B12 levels decreased by 55 pg/mL in women with a history of MBS and by 4.6 pg/mL with a unit increase in body mass index (kg/m2). Furthermore, vitamin D levels in women with a history of MBS decreased by 4.9 ng/mL during pregnancy. Metabolic bariatric surgery is associated with vitamin B12, vitamin D, and iron deficiencies during pregnancy.