In this article, a computationally efficient state estimation method for lithium-ion (Li-ion) batteries is proposed based on a degradation-conscious high-fidelity electrochemical–thermal model for advanced battery management systems. The computational burden caused by the high-dimensional nonlinear nature of the battery model is effectively eased by adopting an ensemble-based state estimator using the singular evolutive interpolated Kalman filter (SEIKF). Unlike the existing schemes, it shows that the proposed algorithm intrinsically ensures mass conservation without imposing additional constraints, leading to a battery state estimator simple to tune and fast to converge. The model uncertainty caused by battery degradation and the measurement errors are properly addressed by the proposed scheme as it adaptively adjusts the error covariance matrices of the SEIKF. The performance of the proposed adaptive ensemble-based Li-ion battery state estimator is examined by comparing it with some well-established nonlinear estimation techniques that have been used previously for battery electrochemical state estimation, and the results show that excellent performance can be provided in terms of accuracy, computational speed, and robustness.