When controlled in an open-loop fashion, both stationary and dynamical diesel engine performance can deteriorate due to disturbances. Although cycle-to-cycle fuel injection control has the potential of reducing the performance degradation by manipulating the fueling profile in real-time, this potential has not been thoroughly studied. This is especially true for multi-pulse fuel injection, due to the lack of a controller design method with closed-loop reference tracking performance guarantees. In this paper, we introduce a systematic design method for multivariable cycle-to-cycle fuel injection control. The design method is based on several local linearizations to address varying combustion behavior due to different engine speeds, torques and disturbances. This leads to a controller that is robust with respect to all the local linearizations. Experimental results show that the controller works well in both stationary and dynamical operating conditions, and has fast dynamical performance (settling time less than 1.5 [s]). Moreover, experimental data shows that cycle-to-cycle fuel injection control is robust against the uncertainties introduced by disturbed rail pressure and swirl valve position.