Background and aims <p>The endophytic communities of plants are significantly influenced by heavy metal stress. Conversely, endophytes contribute to host plants’ heavy metal tolerance and accumulation. This study evaluates the impact of cadmium (Cd) on rice, and investigates the role of endophytes in Cd accumulation in rice.</p> Methods <p>The endophytic bacterial community of rice under Cd stress was investigated using both culture-dependent and culture-independent methods. In addition, the roles of endophytic bacteria in rice yield and Cd accumulation in rice grains were examined.</p> Results <p>The composition of rice endophytic bacterial communities was shaped by both tissue type and soil Cd concentration. Elevated Cd concentration reduced the endophyte alpha diversity, altered the dominant genera, and promoted a less complex co-occurrence network. Partic</p> <p>ularly, specific bacterial endophytes (e.g., <i>Methylocystis</i>, <i>Bradyrhizobium</i> and <i>Brevundimonas</i>) were significantly correlated with grain Cd concentration, suggesting their potential role in regulating Cd accumulation in rice grain. A core microbiota, including <i>Bradyrhizobium</i>, <i>Brevundimonas</i>, <i>Acinetobacter</i>, <i>Agrobacterium</i>, etc. consistently presented across all Cd levels, suggesting their essential, stress-independent functions. Some of them exhibited multiple plant growth-promoting traits and Cd tolerance. Pot experiments showed the strain GCRD9 (<i>Agrobacterium</i> sp.) could promote rice growth and increase thousand-grain weight, while reducing Cd accumulation in grains by 55.6%.</p> Conclusions <p>These findings provide new insights into the soil-crop-endophyte interactions and highlight the potential of specific bacterial strains for developing endophyte-assisted crop strategies to ensure safe crop production under heavy metal stress.</p>