Scientific and technological advances in the field of rotatory electrical machinery are leading to an increased efficiency in those processes and systems in which they are involved. In addition, the consideration of advanced materials, such as hybrid or ceramic bearings, are of high interest towards high-performance rotary electromechanical actuators. Therefore, most of the diagnosis approaches for bearing fault detection are highly dependent of the bearing technology, commonly focused on the metallic bearings. Although the mechanical principles remain as the basis to analyze the characteristic patterns and effects related to the fault appearance, the quantitative response of the vibration pattern considering different bearing technology varies. In this regard, in this work a novel data-driven diagnosis methodology is proposed based on deep feature learning applied to the diagnosis and identification of bearing faults for different bearing technologies, such as metallic, hybrid and ceramic bearings, in electromechanical systems. The proposed methodology consists of three main stages: first, a deep learning-based model, supported by stacked autoencoder structures, is designed with the ability of self-adapting to the extraction of characteristic fault-related features from different signals that are processed in different domains. Second, in a feature fusion stage, information from different domains is integrated to increase the posterior discrimination capabilities during the condition assessment. Third, the bearing assessment is achieved by a simple softmax layer to compute the final classification results. The achieved results show that the proposed diagnosis methodology based on deep feature learning can be effectively applied to the diagnosis and identification of bearing faults for different bearing technologies, such as metallic, hybrid and ceramic bearings, in electromechanical systems. The proposed methodology is validated in front of two different electromechanical systems and the obtained results validate the adaptability and performance of the proposed approach to be considered as a part of the condition-monitoring strategies where different bearing technologies are involved.