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Management of the performance quality attributes and shared computing resources in a web system environment is vital to many business domains in order to achieve business objectives. These systems need to provide agreed levels of quality of service to their clients while allocating limited available resources among them. This paper proposes a new runtime management scheme based on predictive control to manage such systems within defined constraints. It firstly addresses the issue of building a multi-input multi-output (MIMO) system model when the equality constraints on the total amount of resources are considered. Then, the same performance management and resource allocation problem is reformulated with inequality constraints to improve the system model identification and runtime control. With the dynamic model built, the resource management problem in a shared resource environment is solved using model predictive control and constraint optimization. The performance of the proposed control system is validated on a prototype system implementing a real world scenario under different operation conditions.