Background and aims <p>Rhizosphere keystone taxa play important roles in suppressing soilborne disease (e.g., soybean root rot), especially during the critical seedling stage of plant development. However, they can be disrupted by environmental factors, with herbicides residual in soil often overlooked. This study aims to investigate how keystone taxa and their functions respond to herbicide exposure, with particular emphasis on their potential role in soilborne disease onset.</p> Methods <p>A 25-day pot experiment under residual herbicide stress was conducted to track rhizosphere microbial dynamics and plant performance. By combining amplicon and metagenomic sequencing with pathogen quantification, we identified keystone taxa from the rhizosphere networks of two healthiest plants and investigated their links with disease development.</p> Results <p>Herbicide stress increased root rot severity, with elevated DSI evident from the early seedling stage and persisting throughout the period. Notably, herbicide-induced changes in keystone taxa on days 5–7 significantly correlated with final disease severity. Herbicide stress reduced key disease-suppressive pathways (biosynthesis of macrolides, enediyne and vancomycin group antibiotics, and siderophore group nonribosomal peptides), which were potentially associated with DSI variation. These pathways were linked to the identified keystone taxon <i>Streptomyces</i>.</p> Conclusions <p>Days 5–7 was a sensitive period when herbicide stress disrupted keystone taxa and promoted disease development. Maintaining the abundance and stability of keystone taxa during this period is important. This study highlights the ecological importance of early keystone taxa in shaping plant-pathogen interactions under herbicide stress, providing insights for microbiome-based plant protection strategies in sub-healthy agricultural soil.</p> Graphical Abstract <p></p>