Artificial Intelligence (AI), Agricultural Machine Learning (AML) and Deep Learning in Agriculture (ADL) are increasingly applied for crop health monitoring and precision disease management. Huanglongbing (HLB) or citrus greening disease, is among the most destructive citrus diseases worldwide, causing substantial yield and quality losses. This study developed a non-destructive UAV-based multispectral sensing framework for real-time HLB detection and severity classification using spectral signatures and machine learning algorithms. Multispectral imagery was acquired using a Parrot Sequoia sensor mounted on a hexacopter UAV during the peak vegetative stage at Vasantrao Naik Marathwada Krishi Vidyapeeth, Parbhani, India. Spectral information from Green (550 nm), Red (660 nm), Red Edge (735 nm), and Near Infrared (790 nm) bands was used to characterize Healthy, 25% HLB, 50% HLB, 100% HLB, and Background classes. A total of 10,000 multispectral canopy patches (2,000 samples per class; 128 × 128 pixels) were extracted for analysis. Vegetation indices including NDVI, NDRE, and GNDVI were computed to evaluate canopy stress conditions. Random Forest (RF), Support Vector Machine (SVM), and K-Nearest Neighbour (KNN) classifiers were trained and evaluated using multispectral reflectance features. RF achieved the highest overall accuracy (92.45%), followed by KNN (92.05%) and SVM (91.10%), with macro-average precision, recall, and F1-score values of 92%. Multiclass ROC analysis produced micro- and macro-average AUC values of 0.99. Spectral analysis showed higher Red Edge and NIR reflectance in healthy canopies, whereas HLB-infected canopies exhibited increased Red reflectance and reduced NIR response due to chlorophyll degradation and cellular damage. ANOVA confirmed significant differences among classifiers (p < 0.05). UAV-based multispectral sensing enabled rapid and non-destructive detection of Huanglongbing severity in citrus orchards.