This paper aims at studying, the effects of biodiesel-diesel, biodiesel-hydrogen, and diesel-hydrogen fuel blends on engine performance, emissions, and combustion characteristics were investigated in a modified 4-cylinder, turbocharged, common rail direct injection, and compression ignition (CI) engine. Biodiesel was produced from through transesterification of Cynara cardunculus seed oil according to EN 14214 standards with a short-chain alcohol in the presence of a catalyst. The addition of hydrogen as a combustion enhancer used to counteract the increase in emissions and further improve engine performance. Hydrogen was injected in small quantities in the air intake manifold, while diesel-biodiesel blends were injected directly inside the cylinder. Diesel (D), biodiesel (B100), and biodiesel-diesel-hydrogen (B7+H2.5), biodiesel-hydrogen (B100+H2.5), and diesel-hydrogen (D+H2.5) fuel blends were used. Experimental results showed that while maximum engine power and maximum engine torque were obtained with B7+H2.5, the highest thermal efficiency was achieved with B100+H2.5. The lowest specific fuel consumption was obtained as 217 g/kWh at 2000 rpm with diesel. Maximum cylinder pressure and heat release rates were measured as 100.48 bar and 576.12 kJ/m3 deg with diesel fuel at 3000 rpm. The minimum CO emissions were obtained as 0.04% with B100 and B100+H2.5 fuels. CO2 and HC emissions reduced significantly whereas NOx increased, compared to diesel fuel.