A controller for controlling a system with continuous and discrete elements of operation accepts measurements of a current state of the system, solves a mixed-integer model predictive control (MI-MPC) problem subject to state constraints on the state of the system to produce control inputs to the system, and submits the control inputs to the system thereby changing the state of the system. To solve the MI-MPC, the controller transforms the state constraints into state-invariant control constraints on the control inputs to the system, such that any combination of values for the control inputs, resulting in a sequence of values for the state variables that satisfy the state constraints, also satisfy the state-invariant control constraints, and solve the MI-MPC problem subject to the state constraints and the state-invariant control constraints.