The aim of this study was to reveal the effects of four endophytic bacteria (EB) (Ochrobactrum sp. CB36/1, Pantoea agglomerans CC37/2, Bacillus thuringiensis CA41/1 and Pseudomonas fluorescens CC44) on the plant development of tomato and pepper and the effects against bacterial spot disease caused by Xanthomonas euvesicatoria (Xe) in both hosts. EB applied on tomato and pepper seedlings cultivated in a sterile peat growing medium in a climate chamber in two different periods to the roots. The pathogen inoculated on the leaves by spraying. Disease severity was measured by different scales for tomatoes and peppers, and plant development parameters were determined at the end of the study. The antagonistic effects of EB against Xe and 1-Aminocyclopropane-1-carboxylic acid (ACC) deaminase activities were determined with in vitro studies. The effect of endophytic bacteria on tomato and pepper varied according to the host plant x endophyte x pathogen combination. While no bacteria were effective against the pathogen in vitro, Ochrobactrum sp. CB36/1 inhibited the disease severity by 37% in tomato plants, but this effect was not observed in pepper. Tomato and especially pepper plants under disease stress had root and shoot fresh and dry weight increased by 28% to 128% by EB. The measurable effects of EB under biotic stress were determined to be higher than in stress-free conditions. In conclusion, the endophytic bacteria used in the study have potential for use within sustainable integrated agricultural concept framework, with their effects determined to vary according to the host, pathogen and endophytic bacteria.