Many effective plant-microbe interactions lead to biological changes that can stimulate plant growth and production. This study evaluated the effect of the interaction between quinoa (Chenopodium quinoa Willd.) and endophytic bacterial strains on differential responses under biotic stress. Four strains of endophytic bacteria were used to inoculate three quinoa genotypes. Endophytic bacteria, isolated from the endosphere of healthy genotypes of quinoa plants, were used to evaluate their biocontrol activity against Pseudomonas syringae on quinoa plants, which causes leaf spot disease, depending on some different parameters. Quinoa genotype plants were treated with four treatments: pathogenic bacteria only (T1), internal bacteria only (T2), pathogenic bacteria + endogenous bacteria (T3), and untreated as the control (T4). The results indicated that there was a significant difference between chlorophyll content index of infected plants without bioagent (untreated) compared to plants bio-inoculated with endophytic bacteria. The highest mean disease incidence was on the plants without bacterial inoculum (90, 80, and 100%) for quinoa genotypes G1, G2, and G3, respectively. The results showed that there were significant differences in the weight of grains/plant, as the value ranged from 8.1 to 13.3 g when treated with pathogens (T1) compared to the treatment with pathogens and endogenous bacteria (T3), which ranged from 11.7 to 18.6 g/plant. Decreases in total aromatic amino acids appeared due to the pathogen infection, by 6.3, 22.8, and 24.1% (compared to the control) in G1, G2, and G3, respectively. On the other hand, genotype G3 showed the highest response in the levels of total aromatic and total neutral amino acids. The endophytic strains promoted quinoa seedling growth mainly by improving nutrient efficiency. This improvement could not be explained by their ability to induce the production of amino acids, showing that complex interactions might be associated with enhancement of quinoa seedling performance by endophytic bacteria. The endophytic bacterial strains were able to reduce the severity of bacterial leaf spot disease by 30, 40, and 50% in quinoa genotypes G1, G2, and G3, respectively, recording significant differences compared to the negative control. The results indicated that, G1 genotype was superior in different performance indicators (pathogen tolerance index, yield injury %, superiority measure and relative performance) for grain weight/plant under pathogen infection condition when treated with endophyte bacteria. Based on this study, these bacterial strains can be used as a biotechnology tool in quinoa seedling production and biocontrol to diminish the severity of bacterial leaf spot disease.