Nutritional supplementation during pregnancy is increasingly recommended especially in low-resource settings, but its oral health impacts have not been studied. Our aim was to examine whether supplementation with multiple micronutrients (MMN) or small-quantity lipid-based nutrient supplements affects dental caries development or periodontal health in a rural Malawian population. The study was embedded in a controlled iLiNS-DYAD trial that enrolled 1391 pregnant women <20 gestation weeks. Women were provided with one daily iron-folic acid capsule (IFA), one capsule with 18 micronutrients (MMN) or one sachet of lipid-based nutrient supplements (LNS) containing protein, carbohydrates, essential fatty acids and 21 micronutrients. Oral examination of 1024 participants was conducted and panoramic X-ray taken within 6 weeks after delivery. The supplement groups were similar at baseline in average socio-economic, nutritional and health status. At the end of the intervention, the prevalence of caries was 56.7%, 69.1% and 63.3% (P = 0.004), and periodontitis 34.9%, 29.8% and 31.2% (P = 0.338) in the IFA, MMN and LNS groups, respectively. Compared with the IFA group, women in the MMN group had 0.60 (0.18-1.02) and in the LNS group 0.59 (0.17-1.01) higher mean number of caries lesions. In the absence of baseline oral health data, firm conclusions on causality cannot be drawn. However, although not confirmatory, the findings are consistent with a possibility that provision of MMN or LNS may have increased the caries incidence in this target population. Because of the potential public health impacts, further research on the association between gestational nutrient interventions and oral health in low-income settings is needed.