To improve the predictive capacity of system models in the input–output sense, this paper presents a framework for model updating via learning of modeling uncertainties in locally and globally Lipschitz nonlinear systems. First, we introduce a method to extend an existing known model with an uncertainty model so that stability of the extended model is guaranteed in the sense of set invariance and input-to-state stability. To achieve this, we provide two tractable semi-definite programs. These programs allow obtaining optimal uncertainty model parameters for both locally and globally Lipschitz nonlinear models, given uncertainty and state trajectories. Subsequently, in order to extract this data from the available input–output trajectories, we introduce a filter that incorporates an approximated internal model of the uncertainty and asymptotically estimates uncertainty and state realizations. This filter is also synthesized using semi-definite programs with guaranteed robustness with respect to uncertainty model mismatches, disturbances, and noise. Numerical simulations for a large data-set of a roll plane model of a vehicle illustrate the effectiveness and practicality of the proposed methodology in improving model accuracy, while guaranteeing stability.