The U.S. Department of Energy’s Co-Optima initiative has focused on improving fuel economy and vehicle performance while reducing emissions through the simultaneous development of emerging sustainable fuels with beneficial properties and advanced combustion strategies. A major thrust has been the development of advanced compression ignition (ACI) combustion strategies of gasoline range fuels in combination with spark-ignited (SI) combustion in a single engine capable of multi-mode operation to achieve high power density with enhanced part load efficiency. The aim of this study was to further the understanding of how emissions from both ACI and SI strategies operating on the same fuels in the same engine are impacted by different fuel properties. This investigation focused on particulate matter (PM) and gaseous hydrocarbon emissions from 6 different fuels across 3 different combustion modes on the same single-cylinder engine designed for multi-mode operation: SI combustion, partial fuel stratification (PFS), and spark-assisted compression ignition (SACI). In each of these modes, 3 different CA50 phasings were studied such that all 6 fuels could be studied at the same phasings. Three of the six different fuels used were specially formulated in a previous investigation to study the impact of fuel distillation and aromatic content while maintaining the research octane number (RON) and octane sensitivity. Additionally, neat isooctane and two ethanol containing fuels (RD5-87 and Co-Optima E30) were studied. Different fuel and phasing impacts on emissions were observed across the three combustion modes. Fuel properties were found to impact soot PM and particle number more than the CA50 phasing, while the phasing had more impact on NOx emissions. The NOx emissions were reduced in the PFS mode for all fuels compared to SI combustion, but the SACI combustion mode did not reduce NOx emissions. Although PFS produced low soot PM emissions like SI, total PM mass emissions were significantly higher due to large organic carbon (OC) PM mass contribution. Both PFS and SACI had greater particle number emission than SI operation with small nuclei mode particles dominating in PFS compared to large agglomeration particles in SACI.