Plant fungal diseases are one of the most important causes of crop yield losses. Therefore, plant disease identification algorithms have been seen as a useful tool to detect them at early stages to mitigate their effects. Although deep-learning based algorithms can achieve high detection accuracies, they require large and manually annotated image datasets that is not always accessible, specially for rare and new diseases. This study focuses on the development of a plant disease detection algorithm and strategy requiring few plant images (Few-shot learning algorithm). We extend previous work by using a novel challenging dataset containing more than 100,000 images. This dataset includes images of leaves, panicles and stems of five different crops (barley, corn, rape seed, rice, and wheat) for a total of 17 different diseases, where each disease is shown at different disease stages. In this study, we propose a deep metric learning based method to extract latent space representations from plant diseases with just few images by means of a Siamese network and triplet loss function. This enhances previous methods that require a support dataset containing a high number of annotated images to perform metric learning and few-shot classification. The proposed method was compared over a traditional network that was trained with the cross-entropy loss function. Exhaustive experiments have been performed for validating and measuring the benefits of metric learning techniques over classical methods. Results show that the features extracted by the metric learning based approach present better discriminative and clustering properties. Davis-Bouldin index and Silhouette score values have shown that triplet loss network improves the clustering properties with respect to the categorical-cross entropy loss. Overall, triplet loss approach improves the DB index value by 22.7% and Silhouette score value by 166.7% compared to the categorical cross-entropy loss model. Moreover, the F-score parameter obtained from the Siamese network with the triplet loss performs better than classical approaches when there are few images for training, obtaining a 6% improvement in the F-score mean value. Siamese networks with triplet loss have improved the ability to learn different plant diseases using few images of each class. These networks based on metric learning techniques improve clustering and classification results over traditional categorical cross-entropy loss networks for plant disease identification.