In previous works, we introduced a geometric route to define our Ehrenfest statistical dynamics (ESD) and we proved that, for a simple toy model, the resulting ESD does not preserve purity. We now take a step further: we investigate decoherence and pointer basis in the ESD model by considering some uncertainty in the degrees of freedom of a simple but realistic molecular model, consisting of two classical cores and one quantum electron. The Ehrenfest model is sometimes discarded as a valid approximation to nonadiabatic coupled quantum-classical dynamics because it does not describe the decoherence in the quantum subsystem. However, any rigorous statistical analysis of the Ehrenfest dynamics, such as the described ESD formalism, proves that decoherence exists. In this article, decoherence in ESD is studied by measuring the change in the quantum subsystem purity and by analyzing the appearance of the pointer basis to which the system decoheres, which for our example is composed of the eigenstates of the electronic Hamiltonian.