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Pregnancy markedly increases micronutrient demands; however bariatric surgery can compromise dietary micronutrient intake and absorption. International Consensus Guidelines recommend additional micronutrient supplementation during pregnancy following bariatric surgery to prevent deficiencies; however, their efficacy is unknown. This study examined whether women met recommended micronutrient supplementation during pregnancy and explored the relationship between micronutrient intake and deficiency during pregnancy. Pregnant women who had bariatric surgery prior to conception, aged 18–45 years were recruited prospectively before 23 weeks’ gestation and followed until birth. Multiple pass 24-hour diet recalls assessed dietary micronutrient intake. Micronutrient supplementation and adherence was reported pre-pregnancy, at enrollment, and at 28- and 36-weeks gestation. Maternal blood values were obtained from medical records after birth. Logistic regression examined the role of micronutrient intake in the development of biochemical iron, zinc, copper, selenium, folate, and vitamins A, B12, D, and E deficiencies. Sixty-nine women, aged 31 ± 4.8 years, participated. Multivitamin use increased from 38/69 (55%) pre-pregnancy to 55/69 (80%) at enrolment. The proportion meeting supplementation recommendations was low across all micronutrients, ranging from 38/69 (59%) for selenium to 0/69 for vitamin A. Most participants (56/69, 81%) developed a micronutrient deficiency during pregnancy, most commonly iron (49/69, 72%,) and vitamin B12 (38/69, 54%) followed by vitamin A (21/69, 30%) and vitamin D (21/69, 30%). Though micronutrient intake was correlated with micronutrient concentrations during pregnancy, the study was underpowered to detect predictors of deficiency. Bariatric surgery recipients infrequently met supplement recommendations during pregnancy and the relationship between micronutrient intake and deficiency was not clear. Iron, vitamin A, B12 and D deficiencies were common and warrant routine monitoring in antenatal care post-bariatric surgery. International Consensus Guidelines recommend additional micronutrient supplementation for pregnant women with a history of bariatric surgery. This study found that although most women took multivitamin multimineral supplements during pregnancy, these seldom met the doses recommended in the International Consensus Guidelines. The majority of participants (81%, 56/69) experienced at least one micronutrient deficiency during pregnancy, most commonly iron (49/69, 72%) and vitamin B12 (38/69, 54%). Micronutrient supplementation and dietary intake influenced maternal serum concentrations of vitamin D, E, folate and zinc, but did not demonstrate a clear impact on the odds of deficiency.