Abstract. In the first paper of this series we developed a method to construct theoretical, time-dependent and two-component chromosphere models for late-type main sequence stars. The models consist of non-magnetic regions heated by acoustic waves and magnetic flux tube regions heated by magnetic tube waves. By specifying the magnetic filling factor, theoretical models of stellar atmospheres with different chromospheric activity can be calculated. Here, these models are used to simulate the emerging Ca II and Mg II chromospheric emission fluxes and compare them with observations. The comparison shows that the wave heating alone can explain most but not all of the observed range of chromospheric activity. In addition, the results obtained clearly imply that the base of stellar chromospheres is heated by acoustic waves, the heating of the middle and upper chromospheric layers is dominated by magnetic waves associated with magnetic flux tubes, and that other non-wave (e.g., reconnective) heating mechanisms are required to explain the structure of the highest layers of stellar chromospheres.