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Pepper production is a critical component of the global agricultural economy, with exports reaching a remarkable $6.9B in 2023. This underscores the crop’s importance as a major economic driver of export revenue for producing nations. Botrytis cinerea, the causative agent of gray mold, significantly impacts crops like fruits and vegetables, including peppers. Early detection of this pathogen is crucial for a reduction in fungicide reliance and economic loss prevention. Traditionally, visual inspection has been a primary method for detection. However, symptoms often appear after the pathogen has begun to spread. This study employs the Deep Learning algorithm YOLO for single-class segmentation on plant images to extract spatial details of pepper leaves. The dataset included hyperspectral images at discrete wavelengths (460 nm, 540 nm, 640 nm, 775 nm, and 875 nm) from derived vegetation indices (CVI, GNDVI, NDVI, NPCI, and PSRI) and from RGB. At an Intersection over Union with a 0.5 threshold, the Mean Average Precision (mAP50) achieved by the leaf-segmentation solution YOLOv11-Small was 86.4%. The extracted leaf segments were processed by multiple Transformer models, each yielding a descriptor. These descriptors were combined in ensemble and classified into three distinct classes using a K-nearest neighbor, a Long Short-Term Memory (LSTM), and a ResNet solution. The Transformer models that comprised the best ensemble classifier were as follows: the Swin-L (P:4 × 4–W:12 × 12), the ViT-L (P:16 × 16), the VOLO (D:5), and the XCIT-L (L:24–P:16 × 16), with the LSTM-based classification solution on the RGB, CVI, GNDVI, NDVI, and PSRI image sets. The classifier achieved an overall accuracy of 87.42% with an F1-Score of 81.13%. The per-class F1-Scores for the three classes were 85.25%, 66.67%, and 78.26%, respectively. Moreover, for B. cinerea detection during the initial as well as quiescent stages of infection prior to symptom development, qPCR-based methods (RT-qPCR) were used for quantification of in planta fungal biomass and integrated with the findings from the AI approach to offer a comprehensive strategy. The study demonstrates early and accurate detection of B. cinerea on pepper plants by combining segmentation techniques with Transformer model descriptors, ensembled for classification. This approach marks a significant step forward in the detection and management of crop diseases, highlighting the potential to integrate such methods into in situ systems like mobile apps or robots.