Background <p>The native soil microbiome contributes to regulating the root-associated microbiota, root morphology, and plant growth. Using two canola (<i>Brassica napus</i> L.) genotypes contrasting in root size (small-rooted NAM23 and large-rooted NAM37), we investigated how the native soil microbiome influences canola establishment. Plants were grown in rhizoboxes containing gamma-irradiated (microbiome dysbiosis) or untreated (healthy microbiome) soils for 14 days. We evaluated plant growth and profiled bacterial and fungal communities in unplanted soil, rhizosphere soil, and root samples via DNA amplicon sequencing.</p> Results <p>Soil irradiation inhibited canola early growth, severely reducing shoot fresh mass (8 to 10-fold), root fresh mass and root length (3 to 13-fold). As expected, irradiation reduced microbial diversity and altered microbial community structure. The absence of significant soil physicochemical changes post-irradiation suggests that microbiome dysbiosis, rather than nutrient depletion, was the primary driver of plant growth suppression in irradiated soil. This growth suppression correlated with the depletion of potentially beneficial taxa (e.g., <i>Sphingomonas</i>,<i> Alternaria prunicola</i>,<i> Fusarium</i>,<i> Gibberella avenacea</i>, and <i>Humicola nigrescens</i>) and/or the enrichment of detrimental taxa (e.g., <i>Mucilaginibacter</i>, <i>Leifsonia</i>, and <i>Trichoderma atrobrunneum</i>) in both soil and roots. The large-rooted NAM37 outperformed the small-rooted NAM23 only in healthy microbiome-intact soils, but this growth advantage was not observed in unhealthy microbiome-disrupted irradiated soils.</p> Conclusions <p>Our findings directly demonstrate the critical role of a healthy soil microbiome in supporting canola establishment. The absence of growth disparities between genotypes in irradiated soil indicates that plant fitness is not attributed to fixed root phenotypes but a dynamic interplay between intrinsic root traits and the microbiome.</p>