Environmentally friendly, renewable, and green fuels have many benefits over fossil fuels, particularly regarding energy efficiency, in addition to addressing environmental and socioeconomic problems. As a result, green fuels can be used in transportation and power generating applications. Furthermore, being green can ably address the emission-related issues of global warming. In view of the advantages of renewable fuels, two B20 fuel blends obtained from methyl esters of cashew nutshell (CHNOB), jackfruit seed (JACKFSNOB), and jamun seed oils (JAMSOB) were selected to evaluate the performance of a common rail direct injection (CRDI) engine. Compatibility of the nozzle geometry (NG) and combustion chamber shape (CCS) were optimized for increased engine performance. The optimized CCS matched with an increased number of injector nozzle holes in NG showed reasonably improved brake thermal efficiency (BTE), reduced emissions of smoke, HC, and CO, respectively, while NOx increased. Further combustion parameters, such as ignition delay (ID) and combustion duration (CD) reduced, while peak pressure (PP) and heat release rates (HRR) increased at the optimized injection parameters. The CRDI engine powered with JAMSOB B20 showed an increase in BTE of 4–5%, while a significant reduction in HC and CO emissions was obtained compared to JACKFSNOB B20 and CHNOB B20, with increased NOx.