Analysis of stomata density and its configuration based on scanning electron microscopic (SEM) image of a leaf surface, is an effective way to characterize the plant’s behaviour under various environmental stresses (drought, salinity etc.). Existing methods for phenotyping these stomatal traits are often based on manual or semi-automatic labeling and segmentation of SEM images. This is a low-throughput process when large number of SEM images is investigated for statistical analysis. To overcome this limitation, we propose a novel automated pipeline leveraging deep convolutional neural networks for stomata detection and its quantification. The proposed framework shows a superior performance in contrast to the existing stomata detection methods in terms of precision and recall, 0.91 and 0.89 respectively. Furthermore, the morphological traits (i.e. length & width) obtained at stomata quantification step shows a correlation of 0.95 and 0.91 with manually computed traits, resulting in an efficient and high-throughput solution for stomata phenotyping. © Springer Nature Switzerland AG 2019.