Abstract: Ester composition plays a vital role in altering the fuel property, affecting the diesel engine output characteristics. One of the major issues with biodiesel composition is the presence of polyunsaturated methyl esters in its molecule, which lowers the cetane number and increases the nitric oxide emission. Here, the authors have attempted to modify the ester composition of biodiesel fuels in favor of engine characteristics. The ester compositions were modified through partial hydrogenation process using Pd/C as the catalyst, and the end product is termed as modified methyl esters or partially hydrogenated esters. The 1H NMR spectral data were used to calculate the conversion efficiency of hydrogenation process. Therefore, this paper presents a comprehensive experimental investigation for analyzing the combustion and emission characteristics of methyl esters and modified methyl esters in an automotive diesel engine. The turbocharged CRDI engine was operated at 2250 rpm under four engine loads with 20% (by vol.) blends of methyl ester and modified methyl esters. The test fuels include the baseline diesel, karanja and waste cooking oil. Upon partial hydrogenation, the ester composition changed significantly and lowered the polyunsaturation with a corresponding increase in the saturation factor. A significant difference in ignition delay and nitric oxide emission were observed with a marginal increase in efficiency for the modified methyl esters compared to the blends of methyl esters. Graphic abstract: [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.