Biofuels produced from nonedible sources that are cultivated on marginal lands represent a viable source of renewable and carbon-neutral energy. In this context, biodiesel obtained from Jatropha and Karanja oil seeds have received significant interest, especially in South Asian subcontinent. Both of these fuels are produced from nonedible plant seeds with high oil content, which can be grown on marginal lands. In this research, we have investigated the performance and emission characteristics of Jatropha and Karanja methyl esters (biodiesel) and their blends with diesel. Another objective is to examine the effect of long-term storage on biodiesel's oxidative stability. The biodiesels were produced at Indian Institute of Technology Kanpur, (IIT Kanpur), India, and the engine experiments were performed in a single cylinder, four-stroke, compression ignition engine at Argonne National Laboratory (ANL), Chicago. An endoscope was used to visualize in-cylinder combustion events and examine the soot distribution. The effects of fuel and start of injection (SOI) on engine performance and emissions were investigated. Results indicated that ignition delay was shorter with biodiesel. Consequently, the cylinder pressure and premixed heat release were higher for diesel compared to biodiesel. Engine performance data for biodiesel (J100, K100) and biodiesel blends (J30, K30) showed an increase in brake thermal efficiency (BTE) (10.9%, 7.6% for biodiesel and blend, respectively), brake specific fuel consumption (BSFC) (13.1% and 5.6%), and nitrogen oxides (NOx) emission (9.8% and 12.9%), and a reduction in brake specific hydrocarbon emission (BSHC) (8.64% and 12.9%), and brake specific CO emission (BSCO) (15.56% and 4.0%). The soot analysis from optical images qualitatively showed that biodiesel and blends produced less soot compared to diesel. The temperature profiles obtained from optical imaging further supported higher NOx in biodiesels and their blends compared to diesel. Additionally, the data indicated that retarding the injection timing leads to higher BSFC, but lower flame temperatures and NOx levels along with higher soot formation for all test fuels. The physicochemical properties such as fatty acid profile, cetane number, and oxygen content in biodiesels support the observed combustion and emission characteristics of the fuels tested in this study. Finally, the effect of long-term storage is found to increase the glycerol content, acid value, and cetane number of the two biodiesels, indicating some oxidation of unsaturated fatty acids in the fuels.