This paper is the second part of a study initiated with the paper S. Fiori, "Extended Hamiltonian learning on Riemannian manifolds: Theoretical aspects," IEEE Trans. Neural Netw., vol. 22, no. 5, pp. 687-700, May 2011, which aimed at introducing a general framework to develop a theory of learning on differentiable manifolds by extended Hamiltonian stationary-action principle. This paper discusses the numerical implementation of the extended Hamiltonian learning paradigm by making use of notions from geometric numerical integration to numerically solve differential equations on manifolds. The general-purpose integration schemes and the discussion of several cases of interest show that the implementation of the dynamical learning equations exhibits a rich structure. The behavior of the discussed learning paradigm is illustrated via several numerical examples and discussions of case studies. The numerical examples confirm the theoretical developments presented in this paper as well as in its first part.