Young children are at increased risk for respiratory tract infections and are frequently colonized by respiratory pathogens. However, how the mucosal immune system differs between children and adults is relatively unknown. We collected nasal samples from 50 young children (aged 1-5 years) and 318 young adults (aged 18-34 years) to study how the mucosal immune system and host-microbe interactions differ with age. We used multi-omics data integration to combine host (immunophenotyping, transcriptomic, and cytokines) and microbial (16S-rRNA amplicon sequencing, viral PCRs, and pneumococcal culture) datasets. Young children had a paucity of mucosal granulocytes, while B and T cell subsets were increased. Children also had increased immune activation and inflammation, which associated with the presence of Haemophilus spp. and pneumococcus, but not viruses. In adults, Haemophilus spp. associated with T cell and monocyte recruitment, while Dolosigranulum negatively associated with neutrophil degranulation. Thus, nasal immune composition and host-pathogen interactions were clearly age dependent.