In this study, the combined effect of the piston bowl geometry and fuel injection pressures on combustion, performance and emission characteristics of compression ignition (CI) engine fueled with baseline Diesel (D100) and microalgae-biodiesel (MA100) was studied. In this paper, the comparison study for the two different piston bowl geometry, namely: hemispherical combustion chamber (HCC) and toroidal re-entrant combustion chamber (TRCC), was carried out with the various fuel injection pressures (200-240 bar) performed. A single-cylinder, direct injection, and four strokes were chosen to simulate the compression ignition (CI) engine by developing a zero-dimensional simulation model using Diesel-RK commercial software. The data was validated by comparing the results against experimental data, which showed that the results obtained from the numerical simulation were in good agreement with the experimental results. MPRR, EGT, HRR, BTE, and NOx exhibited an increase with increased fuel injection pressure, while an inverse trend was observed with ID, CO, and HC. When using MA100 biodiesel with HCC piston bowl geometry at fuel injection pressure (200 bar), the maximum predicted brake specific fuel consumption (BSFC) was 0.545 kg/kWh. A significant reduction of nitrogen (NOx) oxides emissions was also observed with low fuel injection pressures. In contrast, the emission characteristics such as hydrocarbons and CO were enhanced by increasing fuel injection pressure and modifying the piston bowl geometry.