Based on the exact factorization of the electron-nuclear wave function, we have recently proposed a mixed quantum-classical scheme [A. Abedi, F. Agostini, and E. K. U. Gross, Europhys. Lett. 106, 33001 (2014)] to deal with non-adiabatic processes. Here we present a comprehensive description of the formalism, including the full derivation of the equations of motion. Numerical results are presented for a model system for non-adiabatic charge transfer in order to test the performance of the method and to validate the underlying approximations.