Natural growth is eliminated by the process of globalization in today’s globe owing to the development of technology and landscapes. The majority of today’s youngsters, as well as our seniors, lack an appropriate understanding of natural species such as plant names, tree names, and medicinal plants. This is attributed to technological advancements and a decline in gardening interest. To close this gap, horticulture may employ technology that aids in the improvement of plant understanding and growth. This method is implemented in the existing system for diagnosing leaf diseases using image processing and machine learning techniques. In the existing process, the classification of leaf disease is performed using image processing steps, such as preprocessing, segmentation, feature extraction, feature reduction, and classification. Even though it utilizes multiple processing steps and region-based classification, it identifies only the type of disease. In this paper, a combined approach of regional-based convolutional neural networks and U-Net (CRUN) is proposed for segmenting the leaf diseases from the augmented leaf dataset. Then, the segmented images are subjected to a morphological process to identify the level of disease in the leaf. This identification helps to identify the leaf’s nature and suggests a process to reduce the disease’s spread to other leaves through the proper use of fertilizers. The proposed method is applied to real-time images of sugarcane leaf diseases, such as bacterial blight and red rot, and banana leaf diseases, such as yellow and black sigatoka. This method is also applied to public sugarcane and banana leaf datasets from the Kaggle website. The proposed CRUN algorithm effectively segments the disease region. The morphological process helps to identify the disease level and protect the plant from further spread of disease. As a result, the proposed CRUN and morphological tests are most effective for automating leaf disease detection and prevention.