Aims <p>Continuous cropping of Lanzhou lily disrupts rhizosphere microecosystem balance, severely compromising bulb quality. This study aims to explore the effect of plant growth-promoting rhizobacteria (PGPR) consortium with amino acids (AAs) on continuous cropping obstacles and to elucidate the regulatory mechanisms of rhizosphere microbiota and bulb metabolism.</p> Methods <p>A three-year field experiment compared three treatments: control (CK), PGPR consortium (T1), and PGPR consortium with AAs (T2). The study evaluated soil enzymes and physicochemical factors, bulb yield and quality index, microbial community, and metabolite spectrum.</p> Results <p>The PGPR consortium improved agronomic performance and rhizosphere function, and the effect is further enhanced after adding AAs. Compared to CK, T1 and T2 significantly increased bulb yield by 20.78% And 28.29%, respectively. Both treatments enhanced bulb polysaccharides, proteins, and saponins, and reduced soil pH and organic matter (OM) content. T1 and T2 promoted beneficial bacteria (<i>TRA3-20, Ellin6055</i>, and <i>Gaiella</i>), and suppressed pathogenic fungi (<i>Cadophora</i>). T2 enriched keystone taxa (<i>MND1</i> and <i>Nitrospira</i>) while reducing pathogens (<i>Acremonium</i> and <i>Ilyonectria</i>). Metabolomics revealed that T1 and T2 altered cyanoamino acid metabolism, increasing stress-responsive metabolites (L-valine and L-isoleucine) and enhanced active substances such as L-ascorbic acid and trigonelline. T2 also elevated organic acids and modulated C5-branched dibasic acid metabolism, facilitating sugar accumulation.</p> Conclusion <p>The integration of PGPR consortium with AAs markedly influenced the restructuring of the rhizosphere microbiome and bulb metabolic activity. This study elucidates the interactions between keystone microbial taxa and host metabolic processes, laying the groundwork for novel strategies to address continuous cropping challenges in Lanzhou lily.</p>