An antibacterial and plant growth promoting nanoemulsion was formulated using thymol, an essential oil component of plant and Quillaja saponin, a glycoside surfactant of Quillaja tree. The emulsion was prepared by a sonication method. Fifty minutes of sonication delivered a long term stable thymol nanoemulsion which was characterized by dynamic light scattering (DLS), transmission electron microscopy (TEM), cryogenic-field emission scanning electron microscopy (Cryo-FESEM) and fourier transform infra-red (FTIR) spectroscopy. Creaming index, pH and dilution stability were also studied for deliberation of its practical applications. The nanoemulsion (0.01-0.06%, v/v) showed substantial in vitro growth inhibition of Xanthomonas axonopodis pv. glycine of soybean (6.7-0.0 log CFU/ml). In pot experiments, seed treatment and foliar application of the nanoemulsion (0.03-0.06%, v/v) significantly lowered the disease severity (DS) (33.3-3.3%) and increased percent efficacy of disease control (PEDC) (54.9-95.4%) of bacterial pustule in soybean caused by X. axonopodis pv. glycine. Subsequently, significant enhancements of plant growth were also recorded in plants treated with thymol nanoemulsion. This is the first report of a thymol based nanoemulsion obtained using Quillaja saponin as a surfactant. Our study claims that nano scale thymol could be a potential antimicrobial and plant growth promoting agent for agriculture.