Micro-cogeneration with locally produced biogas from waste is a proven technique for supporting the decarbonization process. However, the strongly variable composition of biogas can make its use in internal combustion engines quite challenging. Dual-fuel engines offer advantages over conventional SI and diesel engines, but there are still issues to be addressed, such as the low-load thermodynamic efficiency and nitrogen oxide emissions. In particular, it is highly desirable to reduce NOx directly in the combustion chamber in order to avoid expensive after-treatment systems. This study analyzed the influence of the combustion system, especially the piston bowl geometry and the injector nozzle, on the performance and emissions of a dual-fuel diesel−biogas engine designed for micro-cogeneration (maximum electric power: 50 kW). In detail, four different cylindrical piston bowls characterized by radii of 23, 28, 33 and 38 mm were compared with a conventional omega-shaped diesel bowl. Moreover, the influence of the injector tip position and the jet tilt angle was analyzed over ranges of 2−10 mm and 30−120°, respectively. The goal of the optimization was to find a configuration that was able to reduce the amount of NOx while maintaining high values of brake thermal efficiency at all the engine operating conditions. For this purpose, a 3D-CFD investigation was carried out by means of a customized version of the KIVA-3V code at both full load (BMEP = 8 bar, 3000 rpm, maximum brake power) and partial load (BMEP = 4 bar, 3000 rpm). The novelty of the study consisted of the parametric approach to the problem and the high number of investigated parameters. The results indicated that the standard design of the piston bowl yielded a near-optimal trade-off at full load between the thermodynamic efficiency and pollutant emissions; however, at a lower load, significant advantages could be found by designing a deeper cylindrical bowl with a smaller radius. In particular, a new bowl characterized by a radius of 23 mm was equivalent to the standard one at BMEP = 8 bar, but it yielded a NOx-specific reduction of 38% at BMEP = 4 bar with the same value of BTE.