High emissions of particulate matter from diesel engines presents a serious risk to human health and the environment. The addition of oxygenated molecules to diesel fuels has been shown to reduce soot formation during combustion. Polyoxymethylene ethers (POMEs) are a novel class of oxygenated molecules that can be produced from biomass and that have the potential to be used as soot-reducing diesel fuel blendstocks. However, only a few variations of these molecules have been studied thus far, and those that have been characterized present significant disadvantages that could compromise current liquid fuel systems and diesel engines. Using a variety of structure–activity models, we evaluated 67 POMEs to predict the effects of structural variations on important fuel properties. Prediction accuracy was assessed by comparing predictions with measurements for a subset of structures. Nine POME molecules were identified as having potential to reduce soot formation by over 75% compared to conventional diesel fuels while being compatible with current liquid fuel infrastructure, maintaining optimal engine performance, and presenting a minimal risk to the environment. None of these nine POMEs has been previously identified as a potential diesel blendstock. This is the first evaluation of POMEs as a class of molecules and the results guide research on the synthesis, properties, and engine performance of POMEs.