Maternal diet during pregnancy plays a likely role in infant immune development through both direct nutrient specific immunomodulatory effects and by modulating the composition and metabolic activity of the maternal gut microbiome. Dietary fibers, as major substrates for microbial fermentation, are of interest in this context. This is the first study to examine maternal intakes of different fiber sub-types and subsequent infant allergic disease. In an observational study of 639 mother-infant pairs (all infants had a family history of allergic disease) we examined maternal intakes of total fiber, soluble fiber, insoluble fiber, resistant starch, and prebiotic fiber, by a semi-quantitative food frequency questionnaire at 36-40 weeks' gestation. Infants attended an allergy clinical assessment at 12 months of age, including skin prick testing to common allergens. Higher maternal dietary intakes of resistant starch were associated with reduced doctor diagnosed infant wheeze, adjusted odds ratio (aOR) 0.68 (95% CI 0.49, 0.95, p = 0.02). However, in contrast, higher maternal intakes of resistant starch were associated with higher risk of parent reported eczema aOR 1.27 (95% CI 1.09, 1.49, p < 0.01) and doctor diagnosed eczema aOR 1.19 (95% CI 1.01, 1.41, p = 0.04). In conclusion, maternal resistant starch consumption was differentially associated with infant phenotypes, with reduced risk of infant wheeze, but increased risk of eczema.