Background Allergic lung diseases represent an increasing health burden. As reported, inhaled treatment with synergistic agents ODN M362 and Pam2CSK4 (“Pam2ODN”) protects mice against allergic lung inflammation, including that caused by house dust mite (HDM) extract. By preventing sensitization, Pam2ODN reduces HDM-induced eosinophilic and lymphocytic inflammation, but how Pam2ODN affects interactions of lung epithelial cells, dendritic cells, and T cells has not been established. Methods After a single inhaled dose of Pam2ODN or sham, Balb/c were sensitized and challenged with HDM. BAL fluid was collected for flow cytometry analysis of T cell polarization and eosinophilia, while dendritic cell immune responses were assessed in lung homogenates. Bulk RNA-seq, scRNA-seq, and scATAC-seq were performed after sensitization to assess the effect of Pam2ODN on whole lung and epithelial cell inflammatory immune response. Results Pam2ODN pretreatment reduces eosinophils and Th2 polarization without affecting Th1 or Treg cell counts. Furthermore, Pam2ODN inhibits recruitment of lung monocyte-derived dendritic cells (moDCs) and type 2 migratory dendritic cells (DC2s) while preventing HDM-induced decrease of type 1 migratory dendritic cells (DC1s). Bulk RNA reveals that Pam2ODN restricts the expression of HDM sensitization-induced proinflammatory transcripts. This tolerogenic effect is also reflected at the single-cell level in lung epithelial cells, where proinflammatory transcripts, pathways, and chromatin accessibility are inhibited. Conclusions Pam2ODN reprograms lung epithelial cells to attenuate allergen-induced Th2-promoting cytokines and DCs while maintaining the population of protective DC1s. These findings suggest a strategy to mitigate chronic allergic lung diseases by lung epithelium-targeted immunomodulatory interventions.