The vibration generated by diesel engines may influence air and gaseous fuel mixing in a dual-fuel mode. This study is performed on the manifolds of single- and twin-cylinder engines in a diesel–bioCNG dual-fuel mode. It examines the effect of the engine vibration and variable manifold pressure on the flow behavior of the air–bioCNG mixture. The objective is to observe the flow inside the manifolds and mixture quality at the outlet. The mentioned work has found little attention till date. The computational comparison of the flow characteristics inside the intake manifold of the single-cylinder engine is done for an F-shape manifold of the twin-cylinder engine during suction stroke. The experiments are conducted to record both the engines’ vibration signature and cycle data. For this, the same operating parameters are maintained: compression ratio of 16.5, engine speed of 1500 rpm, engine load range (0 Nm–34 Nm), and 80% bioCNG substitution. It employs the boundary conditions such as the vibration amplitude along three axes, variable manifold pressure, and the mass flowrates of air and bioCNG. The parameters to analyze the mixture flow are pressure, velocity, turbulence, helicity, and mass fraction of CH4. The mixture at the manifold outlet of the single-cylinder engine improved to an average uniformity index of 0.9924, indicating better homogeneity. Further, the manifold of the twin-cylinder engine attained the indexes of 0.1484 and 0.2401 for its two cylinders, showing nonhomogeneity.