In highly flexible and integrated manufacturing systems, such as semiconductor fabs, strong interactions between the equipment condition, operations executed on the various machines and the outgoing product quality necessitate integrated decision making in the domains of maintenance scheduling and production operations. Furthermore, in highly complex manufacturing equipment, the underlying condition is not directly observable and can only be inferred probabilistically from the available sensor readings. In order to deal with interactions between maintenance and production operations in Flexible Manufacturing Systems (FMSs) in which equipment conditions are not perfectly observable, we propose in this paper a decision-making method based on a Partially Observable Markov Decision Processes (POMDP's), yielding an integrated policy in the realms of maintenance scheduling and production sequencing. Optimization was pursued using a metaheuristic method that used the results of discrete-event simulations of the underlying manufacturing system. The new approach is demonstrated in simulations of a generic semiconductor manufacturing cluster tool. The results showed that, regardless of uncertainties in the knowledge of actual equipment conditions, jointly making maintenance and production sequencing decisions consistently outperforms the current practice of making these decisions separately.