Purpose <p>Bio-organic fertilizers derived from beneficial microbial strains offer an effective strategy to reduce chemical fertilizer use in tea cultivation. This study investigated the effects of three novel bio-organic fertilizers on soil quality and tea biochemical composition in tea plantations.</p> Methods <p>A three-year field experiment was conducted with five treatments: an unfertilized control (CK), conventional chemical fertilizer (CF), and three bio-organic fertilizers containing <i>Bacillus megaterium</i> (BMG), <i>B. mucilaginosus</i> (BMU), or <i>B. subtilis</i> (BCL). Soil microbial diversity and community composition were analyzed using high-throughput Illumina sequencing. These microbial profiles were integrated with soil physicochemical properties, enzymatic activities, and tea leaf metabolites—including amino acids and secondary compounds—through a multi-omics approach.</p> Results <p>All bio-organic fertilizers significantly increased soil organic matter content, microbial diversity, and co-occurrence network complexity. BMG and BCL treatments promoted Acidobacteriota abundance, while BMU enhanced Actinobacteriota and Chloroflexi dominance. Metabolomic analysis showed that BMG treatment notably increased the biosynthesis of key amino acids (e.g., aspartate, phenylalanine) and flavonoids (e.g., quercetin, luteolin). Correlation analysis revealed strong associations between microbial shifts and metabolite accumulation driving tea quality. Moreover, BMG significantly elevated total amino acid and flavonoid contents and lowered the phenol-to-amino acid ratio, contributing to improved tea quality.</p> Conclusions <p>The bio-organic fertilizer containing <i>B. megaterium</i> substantially enhanced tea quality by selectively promoting key amino acid and flavonoid biosynthesis. These findings demonstrate the potential of microbial-based biofertilizers to improve tea cultivation and provide insights for their optimized design.</p> Graphical abstract <p></p>