Background <p>Accumulation of antibiotics in crops threatens human health. However, the mechanisms and effects of microorganisms on the uptake and accumulation of antibiotics in crops remain poorly understood. This study aimed to investigate the impact and underlying mechanisms of seed-borne microbiota in root on ciprofloxacin (CIP) accumulation in two choy&#xa0;sum varieties through amplicon sequencing, multiple statistical analyses, and subsequent validation of key bacteria via isolation and co-culturing with plants.</p> Results <p>Bacillaceae (mainly <i>Bacillus</i>) was enriched specifically in the roots of CIP high-antibiotic-accumulating variety (HAV) via seed-based vertical transmission activated by the root exudate-derived maleic acid. The relative abundance of Bacillaceae was 9.2 to 27.7 times higher in roots of HAV relative to the low-antibiotic-accumulating variety (LAV). The enrichment of Bacillaceae facilitated a cooperative and beneficial bacterial community formed by the deterministic process. The community in HAV could not only stimulate antioxidase activities and decrease membrane lipid peroxidation via secreting indoleacetic acid and siderophore but also promote its biomass, especially the root length and biomass of HAV, thus greatly improving its tolerance to and absorption of CIP. The variety-specific plant-microbial interactions caused 1.6- to 3.2-fold higher CIP accumulation in shoots of HAV relative to LAV shoots.</p> Conclusions <p>The findings highlight the crucial roles of the seed-borne microbiota in regulating the uptake and accumulation of antibiotics in crops, giving new understanding on the accumulation of organic pollutants in plants, with an emphasis on plant-microbial interactions</p> <p><MediaObject ID="MOESM2"> <VideoObject FileRef="MediaObjects/40168_2025_2073_MOESM2_ESM.mp4" VideoID="8wyrsLJbGysTyA4wSA93PP"> <Caption Language="En" xml:lang="en"> <CaptionContent> <p>Video Abstract</p> </CaptionContent> </Caption> </VideoObject> </MediaObject></p>