Autonomous operation of diesel engines using different military fuels faces many challenges. Engines should be able to use Jet Propellant-8 (JP-8) fuel, as well as alternate and renewable fuels intended to replace petroleum-derived jet or diesel fuels. These fuels can have wide ranges of physical and chemical properties. In addition, diesel engines that power military ground vehicles are originally manufactured for commercial applications which are equipped with additional after treatment devices needed to the meet emission standards. Such devices are not needed in military vehicles. However, commercial engines and after treatment devices are calibrated as one system to meet the emission targets, causing some penalty in fuel economy and peak power. These engines should be recalibrated to produce the highest power density and the best fuel economy required in military vehicles. Furthermore, commercial engines are optimized to operate on ULSD (Ultra Low Sulfur Diesel) fuel, which has narrow specifications. This is not the case in military engines which should be able to operate on JP-8 and other approved alternate fuels which have wide ranges of Cetane Numbers (CN), density, and volatility. It should be noted that all these challenges are related to the combustion process. This paper presents a new technique developed to sense and control the combustion process for different fuels. This technique is based on the ionization in hydrocarbon-air flames. The measured ion current is analyzed in detail to determine the autoignition and combustion characteristic of the fuel used in the engine. This is followed by the development of a control strategy to phase the combustion process of different fuels in order to achieve the targets of improved fuel economy, high power density and reduced soot emissions in military vehicles.