Apparatuses and methods for model quality estimation and model adaptation in multivariable process control are disclosed. A method for updating a multiple input multiple output (MIMO) dynamical model of a process includes perturbing the process, auditing the controller model, identifying poor performing submodels and re-testing the relevant process variables, re-identifying submodels and adapting the model online while the process continues to operate within normal operating parameters. An apparatus comprises an online multivariable controller, a tester, a database to store data corresponding to manipulated variables and controlled variables, and a performance diagnosis module configured to identify problematic submodels and adapt a model used by the controller.