Cercospora leaf spot (CLS) caused by Cercospora beticola is the most destructive leaf disease of sugar beet and may cause high losses in yield and quality. Breeding and cultivation of disease-resistant varieties is an important strategy to control this economically relevant plant disease. Reliable and robust resistance parameters are required to promote breeding progress. CLS lesions on five different sugar beet genotypes incubated under controlled conditions were analyzed for phenotypic differences related to field resistance to C. beticola. Lesions of CLS were rated by classical quantitative and qualitative methods in combination with noninvasive hyperspectral imaging. Calculating the ratio of lesion center to lesion margin, four CLS phenotypes were identified that vary in size and spatial composition. Lesions could be differentiated into subareas based on their spectral characteristics in the range of 400 to 900 nm. Sugar beet genotypes with lower disease severity typically had lesions with smaller centers compared with highly susceptible genotypes. Accordingly, the number of conidia per diseased leaf area on resistant plants was lower. The assessment of lesion phenotypes by hyperspectral imaging with regard to sporulation may be an appropriate method to identify subtle differences in disease resistance. The spectral and spatial analysis of the lesions has the potential to improve the screening process in breeding for CLS resistance.