Food colors are considered the most important component of foodstuff for enhancing the aesthetic appeal of the products. The rapid increase in population raised the demand for food materials, while wastewater from as-related processing industries is used for irrigation. This study was conducted to examine the genotoxicity of industrial wastewater on the plant growth-promoting rhizobacteria (PGPR). Three predominantly used synthetic food colors, including Azorubine E-122, Tartrazine E-102 and Allura Red AC E-129, were used during this project. Rhizobacteria were isolated from agricultural soils and treated with various concentrations of Azorubine E-122, Tartrazine E-102 and Allura red E-129 for a 24 and 48 h duration. DNA extraction and quantification were performed through a modified CTAB method, spectrophotometry and agarose gel electrophoresis. A comet assay was used to check DNA damage. According to the results, all the food colors had caused significant damage to DNA depending upon the concentration and exposure time. The extent of DNA damage caused by Azorubine E-122 was relatively greater compared with the other colors, so the fragmentation rate of 86% and 92% was obtained at 1.25% concentration for 24 and 48 h, respectively. The current results have revealed the devastation capacity of food colors by accelerating distortion risk to soil micro-flora, hence the fertility of the soil.