The benefits of nature exposure for human well-being are well-recognized, yet much remains to be understood about the underlying causal mechanisms. This exploratory, hypothesis-generating pilot study used a natural experimental design with University of Washington students (Seattle, WA, USA; 2024) to investigate links between the nasal microbiome and well-being over an 8-week forest vs. urban environment exposure. After an academic year (September–May) during which all participants (N = 13) were full-time students in Seattle, one group relocated to remote forest sites in western Washington (n = 5; forest condition), while another group remained in urban Seattle (n = 8; urban condition). Self-reported affect, rumination, and mental well-being were assessed pre- and post-exposure using validated surveys, and nasal swabs were collected pre- and post-exposure for nasal microbiome profiling via 16S rRNA gene sequencing. Compared to the urban group, the forest group exhibited significantly greater increases in positive affect and decreases in negative affect and rumination. While no between-group differences in overall nasal bacterial community composition were detected pre-exposure, significant differences emerged post-exposure. Moreover, the forest group exhibited greater post-exposure taxonomic richness at a marginally statistically significant level and significant enrichment of taxa previously associated with well-being (e.g., Bifidobacterium, Akkermansia). These changes were not observed in the urban group. Increases in taxonomic richness and the relative abundance of these key taxa were significantly associated with affective improvements. These preliminary results suggest that nasal microbiome-mediated pathways linking nature exposure with well-being merit further investigation.