Late leaf spot (LLS) is an important disease of peanut, causing global yield losses. Developing resistant varieties through breeding is crucial for yield stability, especially for smallholder farmers. However, traditional phenotyping methods used for resistance selection are laborious and subjective. Remote sensing offers an accurate, objective, and efficient alternative for phenotyping for resistance. The objectives of this study were to compare between regression and classification for breeding, and to identify the best models and indices to be used for selection. We evaluated 223 genotypes in three environments: Serere in 2020, and Nakabango and Nyankpala in 2021. Phenotypic data were collected using visual scores and two handheld sensors: a red–green–blue (RGB) camera and GreenSeeker. RGB indices derived from the images, along with the normalized difference vegetation index (NDVI), were used to model LLS resistance using statistical and machine learning methods. Both regression and classification methods were also evaluated for selection. Random Forest (RF), the artificial neural network (ANN), and k-nearest neighbors (KNNs) were the top-performing algorithms for both regression and classification. The ANN (R²: 0.81, RMSE: 22%) was the best regression algorithm, while the RF was the best classification algorithm for both binary (90%) and multiclass (78% and 73% accuracy) classification. The classification accuracy of the models decreased with the increase in classification classes. NDVI, crop senescence index (CSI), hue, and greenness index were strongly associated with LLS and useful for selection. Our study demonstrates that the integration of remote sensing and machine learning can enhance selection for LLS-resistant genotypes, aiding plant breeders in managing large populations effectively.