Prenatal exposures may be critical for immune system development, with consequences for allergic disease susceptibility. We examined associations of prenatal exposures (nutrient intakes and air pollutants) with allergic disease biomarkers in adolescence. We used data from 857 mother-child pairs in Project Viva, a Massachusetts-based pre-birth cohort. Outcomes of interest at follow-up (median age 12.9 years) were fractional exhaled nitric oxide (FeNO) and total serum IgE. We applied Bayesian Kernel Machine Regression analyses to estimate multivariate exposure-response functions, allowing for exposure interactions. Exposures were expressed as z-scores of log-transformed data and we report effects in % change in FeNO or IgE z-score per increase in exposure from the 25th to 75th percentile. FeNO levels were lower with higher intakes of prenatal vitamin D (-16.15%, 95% CI: -20.38 to -2.88%), folate from foods (-3.86%, 95% CI: -8.33 to 0.83%) and n-3 PUFAs (-9.21%, 95% CI -16.81 to -0.92%). Prenatal air pollutants were associated with higher FeNO and IgE, with the strongest associations detected for PM2.5 with IgE (25.6% increase, 95% CI 9.34% to 44.29%). We identified a potential synergistic interaction (p = 0.02) between vitamin E (food + supplements) and PM2.5; this exposure combination was associated with further increases in FeNO levels.