Background <p>Environmental variations exert substantial influences on gene expression, growth, development, and product quality in field crops. However, the mechanisms underlying how environmental factors regulate tobacco growth, development, and post-curing quality under field conditions remain poorly understood, primarily owing to the complexity of the field environment.</p> Results <p>Our study demonstrates that precipitation serves as a predominant environmental driver that governs rhizosphere microbiome assembly, which subsequently modulates host carbon and nitrogen metabolic pathways, thereby determining nicotine accumulation and leaf irritability. We conducted an integrated multi-omics study across two representative tobacco growing regions (i.e., Chuxiong and Jianshui) in Yunnan, China, which exhibit distinct geographical and climatic conditions. Results revealed precipitation as a critical regulator of nicotine accumulation, with higher precipitation promoting nicotine biosynthesis and lower precipitation favoring sugar compound accumulation. The most pronounced difference between the two regions was the irritancy of cured tobacco leaves in the cultivar Yun87, which positively correlated with total nitrogen content. Crucially, rhizosphere microorganisms, along with climatic and soil abiotic factors (e.g., pH and available mineral elements), modulated nitrogen-containing compounds, including nicotine accumulation, by regulating carbon, nitrogen transport and utilization cycles, suggesting genetic-level interactions within the tobacco plant.</p> Conclusions <p>Our integrated multi-omics approach reveals a complex cross-kingdom network, providing a mechanistic understanding of how environmental cues are transduced into crop quality traits through the rhizosphere microbiome. This study offers insights in guiding targeted agricultural practices and future research on sustainable production of higher-quality tobacco.</p> Graphical abstract <p></p>