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Circulating food metabolites could improve dietary assessments by complementing traditional methods. Here, biomarker candidates of food intake were identified in plasma samples from pregnancy (gestational week 29, N = 579), delivery (mothers, N = 532; infants, N = 348), and four months postpartum (mothers, N = 477; breastfed infants, N = 193) and associated to food intake assessed with semi-quantitative food frequency questionnaires. Families from the Swedish birth cohort Nutritional impact on Immunological maturation during Childhood in relation to the Environment (NICE) were included. Samples were analyzed using untargeted liquid chromatography–mass spectrometry (LC-MS)-based metabolomics. Both exposure and outcome were standardized, and relationships were investigated using a linear regression analysis. The intake of fruits and berries and fruit juice were both positively related to proline betaine levels during pregnancy (fruits and berries, β = 0.23, FDR < 0.001; fruit juice, β = 0.27, FDR < 0.001), at delivery (fruit juice, infants: β = 0.19, FDR = 0.028), and postpartum (fruits and berries, mothers: β = 0.27, FDR < 0.001, infants: β = 0.29, FDR < 0.001; fruit juice, mothers: β = 0.37, FDR < 0.001). Lutein levels were positively related to vegetable intake during pregnancy (β = 0.23, FDR < 0.001) and delivery (mothers: β = 0.24, FDR < 0.001; newborns: β = 0.18, FDR = 0.014) and CMPF with fatty fish intake postpartum (mothers: β = 0.20, FDR < 0.001). No clear relationships were observed with the expected food sources of the remaining metabolites (acetylcarnitine, choline, indole-3-lactic acid, pipecolic acid). Our study suggests that plasma lutein could be useful as a more general food group intake biomarker for vegetables and fruits during pregnancy and delivery. Also, our results suggest the application of proline betaine as an intake biomarker of citrus fruit during gestation and lactation.