Bacillus is one of the main rhizobacteria to have been used as a study model for understanding many processes. However, their impact on photosynthetic metabolism has been poorly studied. The aim of this study was to evaluate the physiological parameters of pepper (Capsicum chinense Jacq.) plants inoculated with Bacillus spp. strains. Pepper seeds were inoculated with Bacillus cereus (K46 strain) and Bacillus spp. (M9 strain; a mixture of B. subtilis and B. amyloliquefaciens), chlorophyll fluorescence and gas exchange were evaluated. The ANOVA (P ≤ 0.05) showed that the maximum photochemical quantum yield of photosystem II (PSII) (Fv/Fm) in plants inoculated with the M9 strain (0.784) increased with respect to other treatments (K46: 0.744 and Control: 0.739). Inoculated plants with M9 and K46 strains exhibited an increase of both photochemical quenching (qP) (by 27% and 24%, respectively) and CO2 assimilation rate (photosynthesis) (by 20% and 16%, respectively), when compared with non-inoculated plants. Furthermore, plants inoculated with M9 and K46 showed decreased transpiration (61% and 57%, respectively) with respect to controls. Likewise, both electron transport rate of PSII (ETR) and PSII operating efficiency (ΦPSII) increased in inoculated plants. However, only plants inoculated with the M9 strain showed enhancements on all growth characteristics. Our results therefore show that inoculating plants with M9 strain positively influenced the performance of the photosynthetic mechanism in pepper plants to increase chlorophyll fluorescence and gas exchange parameters. promotion of photosynthetic capacity in pepper was due to increased ETR in the thylakoid membranes, which was promoted by the bacteria. M9 strain could even be used in sustainable agriculture programs.