Background and aims <p>Continuous cropping and improper fertilization have led to frequent soil-borne diseases, which have seriously affected the yield of vegetables such as cucumbers, posing a major challenge to sustainable agricultural production. Although numerous studies have demonstrated the beneficial role of soil microorganisms in plant growth and health maintenance, their responses to bio-organic fertilizer applications remain unexplored.</p> Methods <p>This study analyzed the effects of organic and bio-organic fertilizers on rhizosphere and non-rhizosphere microbiomes and their associations with cucumber growth, health, and soil fertility through field experiments.</p> Results <p>The results indicated that bio-organic fertilizer treatments (BM1 and BM4) enhanced cucumber dry biomass by 20.39% compared with chemical fertilizer (CF) and organic fertilizer (M1 and M4) treatments. Additionally, both BM1 and BM4 reduced disease severity by 20.08% and improved soil fertility, including soil organic matter and total nitrogen content, while mitigating soil acidification. Furthermore, BM1 and BM4 significantly increased the α-diversity of rhizosphere microbiomes compared with CF. Bio-organic fertilizers enriched the potentially beneficial microbiota, such as <i>Bacillus</i>, <i>Flavobacterium</i>, and <i>Pseudomonas</i>, while reducing pathogens, including <i>Fusarium</i> and <i>Lectera</i>. Network analysis indicated higher complexity and stability of rhizosphere microbial networks in BM1 and BM4 than those in CF or M. Analyses revealed that the beneficial rhizosphere taxa, pathogens, and microbial network characteristics strongly predicted plant growth, disease severity, and soil fertility indicators.</p> Conclusions <p>Above all, bio-organic fertilizers can enhance vegetable production performance by regulating the rhizosphere microbiome, which provides a foundation for screening biocontrol strains to improve productivity.</p>