Starting with the exact factorization of the molecular wavefunction, this paper presents the results from the numerical implementation in nonadiabatic molecular dynamics of the recently proposed bohmion method. Within the context of quantum hydrodynamics, we introduce a regularized nuclear Bohm potential admitting solutions comprising a train of $delta$-functions which provide a finite-dimensional sampling of the hydrodynamic flow paths. The bohmion method inherits all the basic conservation laws from its underlying variational structure and captures electronic decoherence. After reviewing the general theory, the method is applied to the well-known Tully models, which are used here as benchmark problems. In the present case of study, we show that the new method accurately reproduces both electronic decoherence and nuclear population dynamics.