In this study, real-time disease monitoring was conducted on onion which is the most representative crop in Republic of Korea, using an image acquisition system newly developed for the mobile measurement of phenotype. The purpose of this study was to improve the accuracy of prediction of disease and state variables by processing images acquired from monitoring. The image acquisition system was consisted of two parts, a motorized driving system and a PTZ (pan, tilt and zoom) camera to take images of the plants. The acquired images were processed as follows. Noise was removed through an image filter and RGB (red, green and blue) colors were converted to HSV (hue, saturation and value), which enabled thresholding of areas with different colors and properties for image binarization by comparing the color of onion leaf with ambient areas. Four objects with the most significant browning in the onion leaf to the naked eye were selected as the samples for data acquired. The thresholding method with image processing was found to be superior to the naked eye in identifying accurate disease areas. In addition, it was found that the incidence of disease was different in each disease area ratio. As a result, the use of image acquisition system in image processing analysis will enable more prompt detection of any changes in the onion and monitoring of disease outbreaks during the crop lifecycle.