Uncertainty remains regarding the effects of outdoor air pollution in rural areas on childhood asthma, rhinitis, and eczema. Although these diseases often coexist, few studies have examined the effects of air pollution on their multimorbidity. The objective of this study was to investigate the associations of pregnancy exposure to outdoor fine particulate matter (PM2.5) and nitrogen dioxide (NO2) with childhood asthma, rhinitis, eczema, and their multimorbidity. We included children from the 6-year (n = 1322) and 12-year (n = 1118) follow-up of the Pélagie mother-child cohort in Brittany, France where 64% of the participants lived in rural areas. Asthma, rhinitis, eczema, and a multimorbidity phenotype (concomitant presence of ≥2 diseases) were defined by validated questionnaires. PM2.5 and NO2 concentrations during pregnancy were modeled at residential address using land use regression. We assessed associations using logistic regressions per interquartile range (PM2.5: 3 μg/m3; NO2: 10 μg/m3). We also performed stratification by type of area (urban and rural). Asthma, rhinitis, eczema, and the multimorbidity phenotype prevalence were 12%, 20%, 22% and 12% at 6-years, and 10%, 23%, 19% and 11% at 12-years of follow-up. At 6-years, for eczema, a tendency of an association was observed with NO2 (OR = 1.15, 95% CI = 0.97-1.36, p-value = 0.10), and stratification by type of area showed statistically significant associations for PM2.5 (1.49 (1.03-2.13), p = 0.03) and NO2 (1.40 (1.08-1.82), p = 0.01) in the urban stratum. At 12-years, main analyses showed a tendency of associations of PM2.5 (1.38 (0.98-1.93), p = 0.07) and NO2 (1.25 (0.98-1.59), p = 0.07) with asthma, and of NO2 with the multimorbidity phenotype (1.23 (0.97-1.56), p = 0.09). While overall results were not statistically significant, associations in urban settings were stronger than in rural ones at 6-years suggesting that possible differences between the effects in urban and rural areas should be further explored.