This work investigates non-traditional operating modes of a diesel engine that allow the tailoring of acoustic, smoke and thermal signatures for unique unmanned ground vehicle (UGV) military applications. A production, air-cooled single-cylinder diesel engine having a mechanical fuel injection system has been retrofit with a flexible common-rail injection and electronic control system. The experimental domain explores the effects of the injection timing and pressure on the engine’s acoustic, smoke and heat signatures through analysis of the in-cylinder combustion processes. Surface maps of loudness, exhaust temperature and exhaust smoke density over the range of fuel injection strategies are presented, illustrating the degree to which each signature may be controlled. Trade-offs between the signature modes are presented and discussed. The results demonstrate the possibility of providing military UGVs the capability to tailor their acoustic, infrared and smoke signatures independent of speed and load, through an injection system retrofit and control strategy.