Peperomia pellucida L. Kunth is a herb well-known for its secondary metabolites (SM) with biological potential. In this study, the variations in the SM of P. pellucida during association with rhizobacteria were evaluated. Plants were inoculated with Enterobacter asburiae and Klebsiella variicola, which were identified by sequencing of the 16S rRNA gene. The data were evaluated at 7, 21, and 30-day post inoculation (dpi). Plant-bacteria symbiosis improved plant growth and weight. Total phenolic content and phenylalanine ammonia lyase enzyme activity had a significant increase mainly at 30 dpi. P. pellucida was mainly composed of phenylpropanoids (37.30–52.28%) and sesquiterpene hydrocarbons (39.28–49.42%). The phenylpropanoid derivative 2,4,5-trimethoxy-styrene (ArC2), the sesquiterpene hydrocarbon ishwarane, and the phenylpropanoid dillapiole were the major compounds. Principal component analysis (PCA) of the classes and compounds ≥ 2.0% indicated that plants colonized by E. asburiae had a reduction in the content of sesquiterpene hydrocarbons and an increase in phenylpropanoids and derivatives. Plants treated with this bacterium also had an increase in the content of 2,4,5-trimethoxystyrene at 30 dpi. Plants inoculated with K. variicola had significant increases only in the content of the classes monoterpene hydrocarbons and ‘other compounds’ (hydrocarbons, esters, ketones, etc.). These data suggest that the production of plant secondary metabolites can be modified depending on the type of rhizobacteria inoculated.