Abstract Plant root border cells (RBCs) prevent the colonization of plant growth‐promoting rhizobacteria (PGPR) at the root tip, rendering the PGPR unable to effectively control pathogens infecting the root tip. In this study, we engineered four strains of Pseudomonas sp. UW4, a typical PGPR strain, each carrying an enhanced green fluorescent protein (EGFP)‐expressing plasmid. The UW4E strain harboured only the plasmid, whereas the UW4E‐flg22 strain expressed a secreted EGFP‐Flg22 fusion protein, the UW4E‐Flg(flg22) strain expressed a non‐secreted Flg22, and the UW4E‐flg22‐D strain expressed a secreted Flg22‐DNase fusion protein. UW4E‐flg22 and UW4E‐flg22‐D, which secreted Flg22, induced an immune response in wheat RBCs and colonized wheat root tips, whereas the other strains, which did not secrete Flg22, failed to elicit this response and did not colonize wheat root tips. The immune response revealed that wheat RBCs synthesized mucilage, extracellular DNA, and reactive oxygen species. Furthermore, the Flg22‐secreting strains showed a 33.8%–93.8% higher colonization of wheat root tips and reduced the root rot incidence caused by Rhizoctonia solani and Fusarium pseudograminearum by 24.6%–35.7% compared to the non‐Flg22‐secreting strains in pot trials. There was a negative correlation between the incidence of wheat root rot and colonization of wheat root tips by these strains. In contrast, wheat root length and dry weight were positively correlated with the colonization of wheat root tips by these strains. These results demonstrate that engineered secretion of Flg22 by PGPR is an effective strategy for controlling root rot and improving plant growth.