Abstract Background: Human microbiota have many functions that could contribute to cancer initiation and/or progression at local sites, yet the relation of the lung microbiota to lung cancer prognosis has not been studied. Methods: In a pilot study, 16S rRNA gene sequencing was performed on paired lung tumor and remote normal samples from the same lobe/segment in 19 patients with non–small cell lung cancer (NSCLC). We explored associations of tumor or normal tissue microbiome diversity and composition with recurrence-free (RFS) and disease-free survival (DFS), and compared microbiome diversity and composition between paired tumor and normal samples. Results: Higher richness and diversity in normal tissue were associated with reduced RFS (richness P = 0.08, Shannon index P = 0.03) and DFS (richness P = 0.03, Shannon index P = 0.02), as was normal tissue overall microbiome composition (Bray–Curtis P = 0.09 for RFS and P = 0.02 for DFS). In normal tissue, greater abundance of family Koribacteraceae was associated with increased RFS and DFS, whereas greater abundance of families Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae were associated with reduced RFS or DFS (P < 0.05). Tumor tissue diversity and overall composition were not associated with RFS or DFS. Tumor tissue had lower richness and diversity (P ≤ 0.0001) than paired normal tissue, though overall microbiome composition did not differ between the paired samples. Conclusions: We demonstrate, for the first time, a potential relationship between the normal lung microbiota and lung cancer prognosis, which requires confirmation in a larger study. Impact: Definition of bacterial biomarkers of prognosis may lead to improved survival outcomes for patients with lung cancer.