Compression ignition (CI) engines have good performance but more exhaust emissions. Dual fuel (DF) engines have better performance and lower emissions compared to CI mode. Also, the scarcity of fossil fuels made the researchers to find alternative fuels to power CI engines. Therefore, the present work aims to use hydrogen (H2) and honne oil biodiesel (BHO) to investigate the performance of CI engines in DF mode. Also, it aims to compare the performance of CI engines in various DF modes, namely induction, manifold injection, and port injection. First, the CI engine was fuelled completely by diesel fuel and BHO. The data were gathered when the engine ran at a constant engine speed of 1500 rpm and at 80% load. Second, the CI engine was operated in various DF modes and data were generated. CI engine operation in DF mode was smooth with biodiesel and H2. The brake thermal efficiency (BTE) of 32% and 31.1% was reported with diesel and biodiesel, respectively, for manifold injection due to low energy content and high viscosity of biodiesel. These values were higher than CI mode and other DF modes. Fuel substitution percentage for DF manifold injection was 60% and 57% with diesel and biodiesel, respectively. Smoke, hydrocarbon (HC), and carbon monoxide (CO) emissions were lower than conventional mode, but a reverse trend was observed for oxides of nitrogen (NOx) emissions. Heat release rate (HRR) and peak pressure (PP) were higher than conventional mode due to the fast combustion rate of hydrogen. The shortest ignition delay (ID) period was noticed for traditional diesel fuel, but it was longer for BHO biodiesel due to its higher viscosity and lower cetane number. On the contrary, the presence of hydrogen led to an increment in the combustion duration (CD) owing to the scarcity of oxygen in CD. Consequently, the paper clearly showed that the injection way of hydrogen plays a respectable role in the engine characteristics.