Endophytic bacteria are a group of microorganisms that can intercellularly colonize plant hosts without causing apparent damage or disease. Our previous works found that a pyrroloquinoline quinone (PQQ)-producing endophyte could promote plant growth and systemic tolerance. To demonstrate this PQQ-producing endophyte’s beneficial role in plants, a set of five PQQ synthesis genes from Gluconobacter oxydans was introduced into both Escherichia coli JM109 and Bacillus subtilis RM125, a BsuM-deficient mutant of laboratory strain B. subtilis 168. Interestingly, both strains harboring the PQQ synthesis genes exhibited significantly higher optimal optical density than control strains. In a carbon flux analysis, both strains showed a noticeable increase in their citric acid, alpha-ketoglutaric acid, and succinic acid levels. Conversely, in E. coli, pyruvic acid, malic acid, and fumaric acid levels decreased. These results suggest that PQQ impacts various host species differently. Furthermore, the presence of PQQ in fermentation broth was also confirmed in the RM125 PQQ synthesis recombinant strain. Subsequent experiments by inoculating those Bacillus strains revealed that the laboratory host strain could function as an endophyte, and the PQQ transgenic strain could further promote the growth of Arabidopsis thaliana and increase the number of siliques. These findings confirm PQQ’s vital role in endophyte-mediated plant growth promotion and also suggest the potential of B. subtilis transformed with PQQ genes as an engineered endophyte for studying PQQ’s biological functions in plants. This research is a step forward in understanding how specific substances can beneficially influence plant growth and systemic tolerance through endophytic mechanisms.