Biodiesel is a renewable, domestically produced fuel that has been shown to reduce particulate, hydrocarbon, and carbon monoxide emissions from diesel engines. Under some conditions, however, biodiesel produced from certain feedstocks has been shown to cause an increase in nitrogen oxides (NOx). This is of special concern in urban areas that are subject to strict environmental regulations. Although soy-based biodiesel may increase the emission of nitrogen oxides, it is the most easily accessible in North America. We investigated two routes to reformulate soy-based biodiesel in an effort to reduce nitrogen oxide emissions. In one of these, soy-oil methyl esters were modified by conversion of a proportion of the cis bonds in the fatty acid chains of its methyl esters to their trans isomers. In the other approach, polyol derivatives of soybean oil were transesterified to form soy methyl polyol fatty acid esters. The NOx emissions of these modified biodiesels were then examined, using a Yanmar L100 single cylinder, four stroke, naturally aspirated, air cooled, direct injection diesel engine. Using either isomerized methyl oleate or isomerized soy biodiesel, at 20% blend level in petroleum diesel (‘B20’), nitrogen oxide emissions were elevated by between 1.5 and 3 percentage points relative to the combustion of a B20 blend of commercial biodiesel. Nitrogen oxide emissions were reduced in proportion to blend level during the combustion of polyol biodiesel, with a 20% blend in petrodiesel resulting in a reduction of about 4.5 percentage points relative to the emissions of a comparable blend of commercial soy biodiesel.