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Simple Summary An established dataset of histopathology images obtained by biopsy and reviewed by two pathologists is used to create a two-stage oral squamous cell carcinoma diagnostic AI-based system. In the first stage, automated multiclass grading of OSCC is performed to improve the objectivity and reproducibility of histopathological examination. Furthermore, in the second stage, semantic segmentation of OSCC on epithelial and stromal tissue is performed in order to assist the clinician in discovering new informative features. Proposed AI-system based on deep convolutional neural networks and preprocessing methods achieved satisfactory results in terms of multiclass grading and segmenting. This research is the first step in analysing the tumor microenvironment, i.e., tumor-stroma ratio and segmentation of the microenvironment cells. Abstract Oral squamous cell carcinoma is most frequent histological neoplasm of head and neck cancers, and although it is localized in a region that is accessible to see and can be detected very early, this usually does not occur. The standard procedure for the diagnosis of oral cancer is based on histopathological examination, however, the main problem in this kind of procedure is tumor heterogeneity where a subjective component of the examination could directly impact patient-specific treatment intervention. For this reason, artificial intelligence (AI) algorithms are widely used as computational aid in the diagnosis for classification and segmentation of tumors, in order to reduce inter- and intra-observer variability. In this research, a two-stage AI-based system for automatic multiclass grading (the first stage) and segmentation of the epithelial and stromal tissue (the second stage) from oral histopathological images is proposed in order to assist the clinician in oral squamous cell carcinoma diagnosis. The integration of Xception and SWT resulted in the highest classification value of 0.963 (σ = 0.042) AUCmacro and 0.966 (σ = 0.027) AUCmicro while using DeepLabv3+ along with Xception_65 as backbone and data preprocessing, semantic segmentation prediction resulted in 0.878 (σ = 0.027) mIOU and 0.955 (σ = 0.014) F1 score. Obtained results reveal that the proposed AI-based system has great potential in the diagnosis of OSCC.