This paper proposes a novel approach to registering deformations of 3D non-rigid objects for Augmented Reality applications. Our prototype is able to handle different types of objects in real-time regardless of their geometry and appearance (with and without texture) with the support of an RGB-D camera. During an automatic offline stage, the model is processed in order to extract the data that serves as input for a physics-based simulation. Using its output, the deformations of the model are estimated by considering the simulated behaviour as a constraint. Furthermore, our framework incorporates a tracking method based on templates in order to detect the object in the scene and continuously update the camera pose without any user intervention. Therefore, it is a complete solution that extends from tracking to deformation formulation for either textured or untextured objects regardless of their geometrical shape. Our proposal focuses on providing a correct visual with a low computational cost. Experiments with real and synthetic data demonstrate the visual accuracy and the performance of our approach.