Title: Model-based Unknown Input Estimation via Partially Observable Markov Decision Processes. Abstract: In the context of condition monitoring for structures and industrial assets, the estimation of unknown inputs, usually referring to acting loads, is of salient importance for guaranteeing safe and performant engineered systems. In this work, we propose a novel method for estimating unknown inputs from measured outputs, particularly for the case of dynamical systems with known or learned dynamics. The objective is to search for those system inputs that will reproduce the actual measured outputs, which can be reformulated as a Partially Observable Markov Decision Process (POMDP) problem and solved with well-established planning algorithms for POMDPs. The cross-entropy method is adopted in this paper for solving the POMDP due to its efficiency and robustness. The proposed method is demonstrated using simulated dynamical systems for structures with known dynamics, as well as a real wind turbine with learned dynamics, which is inferred via use of a Replay Overshooting (RO) scheme, a deep learning-based dynamics method for learning stochastic dynamics.