Cord blood metabolites can be predictive of long-term disease risk, but how levels of different metabolites might vary with respect to maternal diet is not well understood. The aim of this study was to evaluate the associations of different dietary patterns during pregnancy with cord blood metabolites (including glycerophospholipid fatty acids, polar lipids, non-esterified fatty acids, amino acids, and the sum of hexoses). Participants from the German LISA birth cohort study, with available data on targeted cord blood metabolomics and maternal diet, were included (n = 739). Maternal diet during the last 4 weeks of pregnancy was assessed by a non-quantitative food-frequency questionnaire. Using factor analysis, ten dietary patterns were identified, which were used in linear regression models exploring associations with cord blood metabolites. After correction for multiple hypothesis testing and adjustment for basic covariates, “fish and shellfish” was associated with higher glycerophospholipid fatty acid C20:5 n3 and lower C22:5 n6, whereas the “meat and potato” pattern was directly associated with propionylcarnitine (C3:0). The observed associations highlight potential metabolic pathways involved in the early programming of health and disease through maternal diet, as well as the potential for establishing quantitative biomarkers for dietary patterns of pregnant women.