Background Goutallier's fatty infiltration of the supraspinatus muscle is a critical condition in degenerative shoulder disorders. Deep learning research primarily uses manual segmentation and labeling to detect this condition. Employing unsupervised training with a hybrid framework of segmentation and classification could offer an efficient solution.Aim To develop and assess a two-step deep learning model for detecting the region of interest and categorizing the magnetic resonance image (MRI) supraspinatus muscle fatty infiltration according to Goutallier's scale.Materials and methods A retrospective study was performed from January 1, 2019 to September 20, 2020, using 900 MRI T2-weighted images with supraspinatus muscle fatty infiltration diagnoses. A model with two sequential neural networks was implemented and trained. The first sub-model automatically detects the region of interest using a U-Net model. The second sub-model performs a binary classification using the VGG-19 architecture. The model's performance was computed as the average of five-fold cross-validation processes. Loss, accuracy, Dice coefficient (CI. 95%), AU-ROC, sensitivity, and specificity (CI. 95%) were reported.Results Six hundred and six shoulders MRIs were analyzed. The Goutallier distribution was presented as follows: 0 (66.50%); 1 (18.81%); 2 (8.42%); 3 (3.96%); 4 (2.31%). Segmentation results demonstrate high levels of accuracy (0.9977 +/- 0.0002) and Dice score (0.9441 +/- 0.0031), while the classification model also results in high levels of accuracy (0.9731 +/- 0.0230); sensitivity (0.9000 +/- 0.0980); specificity (0.9788 +/- 0.0257); and AUROC (0.9903 +/- 0.0092).Conclusion The two-step training method proposed using a deep learning model demonstrated strong performance in segmentation and classification tasks.