Pesticide gestational exposure may contribute to the development of allergies in childhood, yet evidence on its health impact on urban populations remains limited. This study investigates the association between prenatal exposure to individual and mixed pesticides and allergic outcomes, including asthma, wheezing, and eczema, at age 6 in 387 mother-child pairs from the German prospective cohort LiNA. Forty pesticides and metabolites were detected in urine during pregnancy through nontargeted screening, and 11 were selected (detection rate ≥ 17%) for further analysis. Multivariable logistic regression models adjusted for covariates revealed statistically significant associations between dihydroxy-pyrimethanil and asthma (aOR = 1.35, 95% CI: 1.02–1.79), and fluazifop-desbuthyl and wheezing (aOR = 1.14, 95% CI: 1.01–1.30). No significant associations were observed for eczema. The weighted quantile sum (WQS) regression showed that higher pesticide coexposures significantly increased wheezing odds (aOR = 2.08, 95% CI: 1.21–3.56). The main components of the WQS index were fluazifop-desbuthyl, flonicamid, hydroxy-metazachlor, and terbuthylazine, accounting for 67% of the overall mixture effect. These findings suggest that prenatal exposure to pesticides, likely from dietary sources, may increase the risk of childhood asthma and wheezing. Replication studies in populations with comparable pesticide exposures, along with experimental mechanistic validation, will strengthen the understanding of the observed associations.