Close-range spectral imaging (SI) of agricultural plants is widely performed for digital plant phenotyping. A key task in digital plant phenotyping is the non-destructive and rapid identification of drought stress in plants so as to allow plant breeders to select potential genotypes for breeding drought-resistant plant varieties. Visible and near-infrared SI is a key sensing technique that allows the capture of physicochemical changes occurring in the plant under drought stress. The main challenges are in processing the massive spectral images to extract information relevant for plant breeders to support genotype selection. Hence, this study presents a generic data processing workflow for analysing SI data generated in real-world digital phenotyping experiments to extract meaningful information for decision making by plant breeders. The workflow is a combination of chemometric approaches and deep learning. The usefulness of the proposed workflow is demonstrated on a real-life experiment related to drought stress detection and quantification in Arabidopsis thaliana plants grown in a semi-controlled environment. The results show that the proposed approach is able to detect the presence of drought just 3 days after its induction compared to the well-watered plants. Furthermore, the unsupervised clustering approach provides detailed time-series images where the drought-related changes in plants can be followed visually along the time course. The developed approach facilitates digital phenotyping and can thus accelerate breeding of drought-tolerant plant varieties.