The U.S. Department of Energy’s Co-Optima initiative simultaneous focused on diversifying fuel sources, improving efficiency, and reducing emissions through using novel combustion strategies and sustainable fuel blends. For medium-duty/heavy-duty diesel engines, research in this area has led to the development of a multimode strategy that uses premixed charge compression ignition (PCCI) at low loads and conventional diesel combustion (CDC) at mid–high loads. The aim of this study was to understand how emissions were impacted when using PCCI instead of CDC at low loads and switching to an oxygenated biofuel blend. It provides a detailed speciation of the hydrocarbon (HC) and particulate matter (PM) emissions from a multimode medium-duty engine operating at low loads in PCCI and CDC modes and high loads in CDC. The effect of the oxygenated biofuel blend on emissions was studied at all three mode–load conditions using #2 ULSD and a bio-derived fuel (25% hexyl hexanoate (HHN)) blended in #2 ULSD. The PCCI mode effectively decreased NOx, total HC, and PM/PN emissions, with a substantial decrease in larger particles (≥50 nm). A PM/PN reduction was observed at high loads with the 25% HHN fuel. While the total HC emissions were not impacted by fuel type, the detailed HC analysis exposed changes in the HC’s composition.