Plant stress detection involves the process of Identification, Classification, Quantification, and Prediction (ICQP) in crop stress. Numerous approaches exist for plant stress identification; however, a majority rely on expert personnel or invasive techniques. While expert employees demonstrate proficiency across various plants, this approach demands a substantial workforce to ensure the quality of crops. Conversely, invasive techniques entail leaf dismemberment. To overcome these challenges, an alternative is to employ image processing to interpret areas where plant geometry is observable, eliminating the dependency on skilled labor or the need for crop dismemberment. However, this alternative introduces the challenge of accurately interpreting ambiguous image features. Motivated by the latter, we propose a methodology for plant stress detection using 3D reconstruction and deep learning from a single RGB image. For that, our methodology has three steps. First, the plant recognition step provides the segmentation, location, and delimitation of the crop. Second, we propose a leaf detection analysis to classify and locate the boundaries between the different leaves. Finally, we use a Deep Neural Network (DNN) and the 3D reconstruction for plant stress detection. Experimental results are encouraging, showing that our approach has high performance under real-world scenarios. Also, the proposed methodology has 22.86% higher precision, 24.05% higher recall, and 23.45% higher F1-score than the 2D classification method.