A method includes obtaining information identifying (i) uncertainties associated with multiple time-domain parameters of a model and (ii) time-domain performance specifications for a model-based industrial process controller. The model mathematically represents a MIMO industrial process. The method also includes generating multiple tuning parameters for the controller based on the uncertainties and the time-domain performance specifications. The tuning parameters include vectors of tuning parameters associated with the controller, and each vector includes values associated with different outputs of the industrial process. The time-domain parameters could include a process gain, a time constant, and a time delay for each input-output pair of the model. The time-domain performance specifications could include requirements related to worst-case overshoots, settling times, and total variations. The uncertainties could be specified as intervals in which the time-domain parameters lie.