Aims <p>Plant growth promoting rhizobacteria (PGPRs) are potential candidates for Se biofortification. However, in Se-rich acid soils, the mechanism underlying biofortification, whether it is mainly through the facilitation of bioavailable Se or the development of root system, remains elusive.</p> Methods <p><i>Lelliottia</i> sp. KY49 and <i>Enterobacter</i> sp. EG16, varying in their siderophore and IAA production capacities, were inoculated in pak choi (<i>Brassica rapa</i> ssp. <i>chinensis</i>) cultivated in Se-rich yellow soil. Three inoculation methods were performed: root dipping, injection inoculation, and root-irrigating.</p> Results <p>Plant growth was significant promoted. Specifically, the yield of pak choi increased by 104% (EG16) and 130% (KY49), respectively. Additionally, fine root development, chlorophyll synthesis and POD and SOD activities were also enhanced. There was a positive correlation between plant growth and the IAA producing capacity of PGPRs, and the root-irrigating is more beneficial to plant growth. When EG16 was used, the Se concentration in the aboveground of plant and root increased by 64.9% and 70.0%, respectively. In contrast, there was no significant increase in plant Se concentration when KY49 was applied. Furthermore, the increment of plant-Se concentration (Δ-plant-Se) was positively correlated with both the increment of soil organic matter (Δ-SOM) and the increment of bioavailable Se (Δ-bio-Se). The Δ-bio-Se was probably due to the transformation of organic matter-bound Se (OM-Se) and residual Se (RES-Se) into the soluble Se forms, driven by siderophore production of PGPRs.</p> Conclusions <p>In the Se-rich soils, PGPRs boost soil Se bioavailability by siderophore production and augmentation of SOM, thereby facilitating plant Se bioaccumulation.</p>