In low-temperature combustion concepts such as partially premixed combustion, the ignition delay should be large enough in order to ensure sufficient fuel and air mixing before the start of combustion. It is also necessary that the combustion timing is sufficiently well phased for high thermal efficiency.Since the ignition delay and combustion timing are intimately coupled, the decoupling of these two quantities gives rise to an interesting multiple input, multiple output control problem where the control of the air system and the fuel injection system have to be combined. In a multi-cylinder engine this problem becomes underdetermined or uncontrollable with more outputs than inputs.This article investigates model-based cycle-to-cycle cylinder-individual closed-loop control of the ignition delay and the combustion phasing in a multi-cylinder heavy-duty DI engine running on a gasoline fuel mixture. The controller design of choice was model predictive control (MPC) which is a suitable design for multiple input/output systems with actuator constraints. Ignition delay and combustion phasing were extracted from cooled in-cylinder pressure sensors and controlled by manipulating injection timings, the gas mixture temperature and exhaust-gas recirculation (EGR) ratio using a dual EGR-path system and a fast thermal-management (FTM) system.